[ Started: 2025-09-03 10:45:12 CEST ] [ OmnipathR v3.16.2 for BioC-3.21 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_21 (e923fc4 2025-08-30 11:55:56) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/emmeans_1.11.2-8.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/FactoMineR_2.12.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggraph_2.2.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/SeuratObject_5.2.0.tar.gz' * installing *source* package ‘emmeans’ ... ** this is package ‘emmeans’ version ‘1.11.2-8’ ** package ‘emmeans’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘emmeans’ * removing ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * installing *source* package ‘ggraph’ ... ** this is package ‘ggraph’ version ‘2.2.2’ ** package ‘ggraph’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cactusTree.cpp -o cactusTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c circlePack.cpp -o circlePack.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c dendrogram.cpp -o dendrogram.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c forceBundle.cpp -o forceBundle.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c hTree.cpp -o hTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c iciclePlot.cpp -o iciclePlot.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c lineCutter.cpp -o lineCutter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c nodes.cpp -o nodes.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pathAttr.cpp -o pathAttr.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c treemap.cpp -o treemap.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c unrooted.cpp -o unrooted.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o ggraph.so cactusTree.o circlePack.o cpp11.o dendrogram.o forceBundle.o hTree.o iciclePlot.o lineCutter.o nodes.o pathAttr.o treemap.o unrooted.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-ggraph/00new/ggraph/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggraph’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * installing *source* package ‘SeuratObject’ ... ** this is package ‘SeuratObject’ version ‘5.2.0’ ** package ‘SeuratObject’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20: required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename DstXprType::Scalar = double; typename SrcXprType::Scalar = double]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix; Src = Eigen::SparseMatrix; Func = assign_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:713:13: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenWrap.h:387:24: required from ‘Eigen::SparseMatrix Rcpp::traits::Exporter >::get() [with T = double]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:89:32: required from ‘T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:152:31: required from ‘T Rcpp::as(SEXP) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/InputParameter.h:34:43: required from ‘Rcpp::InputParameter::operator T() [with T = Eigen::SparseMatrix]’ RcppExports.cpp:20:55: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c data_manipulation.cpp -o data_manipulation.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from data_manipulation.cpp:1: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase > >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9: required from ‘class Eigen::internal::SparseTransposeImpl, 1024>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37: required from ‘class Eigen::TransposeImpl, Eigen::Sparse>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose >’ data_manipulation.cpp:27:22: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ data_manipulation.cpp:83:80: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:58:63: required from ‘struct Eigen::internal::unary_evaluator >, Eigen::internal::IteratorBased, double>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::Transpose >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:27:23: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from ‘void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from ‘void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:111:31: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c valid_pointer.c -o valid_pointer.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o SeuratObject.so RcppExports.o data_manipulation.o valid_pointer.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-SeuratObject/00new/SeuratObject/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/spam/libs/spam.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘SeuratObject’ * removing ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ The downloaded source packages are in ‘/tmp/Rtmposn3zd/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘emmeans’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggraph’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘SeuratObject’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'emmeans', 'enrichplot', 'FactoMineR', 'ggraph', 'ggtree', 'SeuratObject', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/emmeans_1.11.2-8.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.12.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/ggraph_2.2.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/SeuratObject_5.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘emmeans’ ... ** this is package ‘emmeans’ version ‘1.11.2-8’ ** package ‘emmeans’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘emmeans’ * removing ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * installing *source* package ‘ggraph’ ... ** this is package ‘ggraph’ version ‘2.2.2’ ** package ‘ggraph’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cactusTree.cpp -o cactusTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c circlePack.cpp -o circlePack.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c dendrogram.cpp -o dendrogram.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c forceBundle.cpp -o forceBundle.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c hTree.cpp -o hTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c iciclePlot.cpp -o iciclePlot.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c lineCutter.cpp -o lineCutter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c nodes.cpp -o nodes.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pathAttr.cpp -o pathAttr.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c treemap.cpp -o treemap.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c unrooted.cpp -o unrooted.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o ggraph.so cactusTree.o circlePack.o cpp11.o dendrogram.o forceBundle.o hTree.o iciclePlot.o lineCutter.o nodes.o pathAttr.o treemap.o unrooted.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-ggraph/00new/ggraph/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggraph’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘SeuratObject’ ... ** this is package ‘SeuratObject’ version ‘5.2.0’ ** package ‘SeuratObject’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20: required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename DstXprType::Scalar = double; typename SrcXprType::Scalar = double]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix; Src = Eigen::SparseMatrix; Func = assign_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:713:13: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenWrap.h:387:24: required from ‘Eigen::SparseMatrix Rcpp::traits::Exporter >::get() [with T = double]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:89:32: required from ‘T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:152:31: required from ‘T Rcpp::as(SEXP) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/InputParameter.h:34:43: required from ‘Rcpp::InputParameter::operator T() [with T = Eigen::SparseMatrix]’ RcppExports.cpp:20:55: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c data_manipulation.cpp -o data_manipulation.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from data_manipulation.cpp:1: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase > >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9: required from ‘class Eigen::internal::SparseTransposeImpl, 1024>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37: required from ‘class Eigen::TransposeImpl, Eigen::Sparse>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose >’ data_manipulation.cpp:27:22: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ data_manipulation.cpp:83:80: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:58:63: required from ‘struct Eigen::internal::unary_evaluator >, Eigen::internal::IteratorBased, double>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::Transpose >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:27:23: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from ‘void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from ‘void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:111:31: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c valid_pointer.c -o valid_pointer.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o SeuratObject.so RcppExports.o data_manipulation.o valid_pointer.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-SeuratObject/00new/SeuratObject/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/spam/libs/spam.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘SeuratObject’ * removing ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ The downloaded source packages are in ‘/tmp/Rtmposn3zd/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘emmeans’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggraph’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘SeuratObject’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status 7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'emmeans', 'enrichplot', 'FactoMineR', 'ggraph', 'ggtree', 'SeuratObject', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/emmeans_1.11.2-8.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.12.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/ggraph_2.2.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/SeuratObject_5.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘emmeans’ ... ** this is package ‘emmeans’ version ‘1.11.2-8’ ** package ‘emmeans’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘emmeans’ * removing ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/emmeans’ * installing *source* package ‘ggraph’ ... ** this is package ‘ggraph’ version ‘2.2.2’ ** package ‘ggraph’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cactusTree.cpp -o cactusTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c circlePack.cpp -o circlePack.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c dendrogram.cpp -o dendrogram.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c forceBundle.cpp -o forceBundle.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c hTree.cpp -o hTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c iciclePlot.cpp -o iciclePlot.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c lineCutter.cpp -o lineCutter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c nodes.cpp -o nodes.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pathAttr.cpp -o pathAttr.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c treemap.cpp -o treemap.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c unrooted.cpp -o unrooted.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o ggraph.so cactusTree.o circlePack.o cpp11.o dendrogram.o forceBundle.o hTree.o iciclePlot.o lineCutter.o nodes.o pathAttr.o treemap.o unrooted.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-ggraph/00new/ggraph/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggraph’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘SeuratObject’ ... ** this is package ‘SeuratObject’ version ‘5.2.0’ ** package ‘SeuratObject’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20: required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename DstXprType::Scalar = double; typename SrcXprType::Scalar = double]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix; Src = Eigen::SparseMatrix; Func = assign_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:713:13: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenWrap.h:387:24: required from ‘Eigen::SparseMatrix Rcpp::traits::Exporter >::get() [with T = double]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:89:32: required from ‘T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/as.h:152:31: required from ‘T Rcpp::as(SEXP) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ /home/omnipath/local/R/4.5-3.21/Rcpp/include/Rcpp/InputParameter.h:34:43: required from ‘Rcpp::InputParameter::operator T() [with T = Eigen::SparseMatrix]’ RcppExports.cpp:20:55: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c data_manipulation.cpp -o data_manipulation.o In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:205, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Dense:1, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:28, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigen.h:25, from data_manipulation.cpp:1: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:174: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:165: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Core:271: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/SparseCore:37, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/Sparse:26, from /home/omnipath/local/R/4.5-3.21/RcppEigen/include/RcppEigenForward.h:29: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase > >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9: required from ‘class Eigen::internal::SparseTransposeImpl, 1024>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37: required from ‘class Eigen::TransposeImpl, Eigen::Sparse>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose >’ data_manipulation.cpp:27:22: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ data_manipulation.cpp:33:26: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ data_manipulation.cpp:83:80: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:58:63: required from ‘struct Eigen::internal::unary_evaluator >, Eigen::internal::IteratorBased, double>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::Transpose >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:27:23: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from ‘void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from ‘void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ data_manipulation.cpp:111:31: required from here /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppEigen/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c valid_pointer.c -o valid_pointer.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o SeuratObject.so RcppExports.o data_manipulation.o valid_pointer.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-SeuratObject/00new/SeuratObject/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/spam/libs/spam.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘SeuratObject’ * removing ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/SeuratObject’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ The downloaded source packages are in ‘/tmp/Rtmposn3zd/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘emmeans’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggraph’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘SeuratObject’ had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status 8: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status ggraph (2.2.1 -> 2.2.2) [CRAN] Installing 1 packages: ggraph trying URL 'https://cran.uni-muenster.de/src/contrib/ggraph_2.2.2.tar.gz' Content type 'application/x-gzip' length 3532489 bytes (3.4 MB) ================================================== downloaded 3.4 MB * installing *source* package ‘ggraph’ ... ** this is package ‘ggraph’ version ‘2.2.2’ ** package ‘ggraph’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cactusTree.cpp -o cactusTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c circlePack.cpp -o circlePack.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c dendrogram.cpp -o dendrogram.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c forceBundle.cpp -o forceBundle.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c hTree.cpp -o hTree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c iciclePlot.cpp -o iciclePlot.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c lineCutter.cpp -o lineCutter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c nodes.cpp -o nodes.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pathAttr.cpp -o pathAttr.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c treemap.cpp -o treemap.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c unrooted.cpp -o unrooted.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o ggraph.so cactusTree.o circlePack.o cpp11.o dendrogram.o forceBundle.o hTree.o iciclePlot.o lineCutter.o nodes.o pathAttr.o treemap.o unrooted.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-ggraph/00new/ggraph/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggraph’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggraph’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggraph’ The downloaded source packages are in ‘/tmp/Rtmposn3zd/downloaded_packages’ Warning message: In i.p(...) : installation of package ‘ggraph’ had non-zero exit status [ Finished: 2025-09-03 10:47:17 CEST ]