[ Started: 2025-05-22 03:20:16 CEST ] [ liana v0.1.14 for BioC-3.21 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' CellChat (NA -> e4f68625b...) [GitHub] OmnipathR (3.16.0 -> fe4d2c2dd...) [GitHub] decoupleR (2.14.0 -> ee886864d...) [GitHub] Downloading GitHub repo sqjin/CellChat@HEAD nloptr (NA -> 2.2.1 ) [CRAN] lme4 (NA -> 1.1-37) [CRAN] pbkrtest (NA -> 0.5.4 ) [CRAN] car (NA -> 3.1-3 ) [CRAN] rstatix (NA -> 0.7.2 ) [CRAN] ggpubr (NA -> 0.6.0 ) [CRAN] Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap Installing 6 packages: nloptr, lme4, pbkrtest, car, rstatix, ggpubr trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.2.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-37.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz' * installing *source* package ‘nloptr’ ... ** this is package ‘nloptr’ version ‘2.2.1’ ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... /usr/bin/cmake using cmake via /usr/bin/cmake using NLopt via local cmake build on x86_64 set CC=gcc set CFLAGS=-I/usr/local/include -fpic -g -O2 set CXX=g++ set CXXFLAGS=-std=gnu++11 -I/usr/local/include -fpic -g -O2 set LDFLAGS=-L/usr/local/lib -- The C compiler identification is GNU 13.3.0 -- The CXX compiler identification is GNU 13.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- NLopt version 2.10.0 -- Looking for getopt.h -- Looking for getopt.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for getpid -- Looking for getpid - found -- Looking for syscall -- Looking for syscall - found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for qsort_r -- Looking for qsort_r - found -- Looking for time -- Looking for time - found -- Looking for copysign -- Looking for copysign - found -- Looking for getopt -- Looking for getopt - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of unsigned long -- Check size of unsigned long - done -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for fpclassify -- Looking for fpclassify - TRUE -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Success -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Failed -- Looking for __cplusplus -- Looking for __cplusplus - found -- Found JNI: /usr/lib/jvm/java-11-openjdk-amd64/include found components: JVM -- Found Java: /usr/bin/java (found suitable version "21.0.7", minimum required is "1.5") -- Configuring done (2.8s) -- Generating done (0.0s) -- Build files have been written to: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt-build [ 2%] Generating nlopt.hpp [ 2%] Built target generate-cpp [ 6%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRect.c.o [ 6%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/direct_wrap.c.o [ 8%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRserial.c.o [ 10%] Building C object 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CMakeFiles/nlopt.dir/src/algs/ags/local_optimizer.cc.o [ 95%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/ags.cc.o [ 97%] Linking CXX static library libnlopt.a [100%] Built target nlopt [ 2%] Built target generate-cpp [100%] Built target nlopt Install the project... -- Install configuration: "Release" -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/pkgconfig/nlopt.pc -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/include/nlopt.h -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/include/nlopt.hpp -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/libnlopt.a -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/share/man/man3/nlopt.3 -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/share/man/man3/nlopt_minimize.3 -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/share/man/man3/nlopt_minimize_constrained.3 -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends.cmake -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends-release.cmake -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfig.cmake -- Installing: /tmp/RtmpQGDkVi/R.INSTALL13d55e57ee9bb0/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfigVersion.cmake Moving nlopt/lib to nlopt/lib mv: cannot move 'nlopt/lib' to a subdirectory of itself, 'nlopt/lib/lib' Copying headers found in src/nlopt/include into inst/include configure: creating ./config.status config.status: creating src/Makevars ** 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"/opt/R-devel/lib/R/include" -DNDEBUG -Inlopt/include -I/usr/local/include -fpic -g -O2 -c dummy.cpp -o dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Inlopt/include -I/usr/local/include -fpic -g -O2 -c init_nloptr.c -o init_nloptr.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Inlopt/include -I/usr/local/include -fpic -g -O2 -c nloptr.c -o nloptr.o g++ -std=gnu++17 -shared -L/usr/local/lib -o nloptr.so dummy.o init_nloptr.o nloptr.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a installing to /home/omnipath/local/R/4.5-3.21/00LOCK-nloptr/00new/nloptr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nloptr) * installing *source* package ‘lme4’ ... ** this is package ‘lme4’ version ‘1.1-37’ ** package ‘lme4’ 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"/opt/R-devel/lib/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' -I'/opt/R-devel/lib/R/library/Matrix/include' -I/usr/local/include -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -c external.cpp -o external.o g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I'/opt/R-devel/lib/R/library/Matrix/include' -I/usr/local/include -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -c glmFamily.cpp -o glmFamily.o g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I'/opt/R-devel/lib/R/library/Matrix/include' -I/usr/local/include -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -c optimizer.cpp -o optimizer.o g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I'/opt/R-devel/lib/R/library/Matrix/include' -I/usr/local/include -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -c predModule.cpp -o predModule.o g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I'/opt/R-devel/lib/R/library/Matrix/include' -I/usr/local/include -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -c respModule.cpp -o respModule.o g++ -std=gnu++17 -shared -L/usr/local/lib -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-lme4/00new/lme4/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lme4) * installing *source* package ‘pbkrtest’ ... ** this is package ‘pbkrtest’ version ‘0.5.4’ ** package ‘pbkrtest’ 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 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pbkrtest) * installing *source* package ‘car’ ... ** this is package ‘car’ version ‘3.1-3’ ** package ‘car’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (car) * installing *source* package ‘rstatix’ ... ** this is package ‘rstatix’ version ‘0.7.2’ ** package ‘rstatix’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rstatix) * installing *source* package ‘ggpubr’ ... ** this is package ‘ggpubr’ version ‘0.6.0’ ** package ‘ggpubr’ 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 ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggpubr) The downloaded source packages are in ‘/tmp/RtmpyUqF9i/downloaded_packages’ ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyUqF9i/remotes13d46e58afebad/sqjin-CellChat-e4f6862/DESCRIPTION’ ... OK * preparing ‘CellChat’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘CellChat_1.6.1.tar.gz’ * installing *source* package ‘CellChat’ ... ** this is package ‘CellChat’ version ‘1.6.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I/usr/local/include -fpic -g -O2 -c CellChat_Rcpp.cpp -o CellChat_Rcpp.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 CellChat_Rcpp.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/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’ CellChat_Rcpp.cpp:9:79: 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’ CellChat_Rcpp.cpp:9:79: 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/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 >’ CellChat_Rcpp.cpp:20:29: 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, Eigen::Transpose >, 2> >’: /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Product.h:145:7: required from ‘class Eigen::ProductImpl, Eigen::Transpose >, 2, Eigen::Sparse>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/Core/Product.h:71:7: required from ‘class Eigen::Product, Eigen::Transpose >, 2>’ CellChat_Rcpp.cpp:20:31: 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/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/Eigen/src/SparseCore/SparseMatrix.h:1040:66: 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]’ CellChat_Rcpp.cpp:19:22: 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/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]’ CellChat_Rcpp.cpp:19:22: 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/SparseUtil.h:121:8: required from ‘struct Eigen::internal::plain_object_eval, Eigen::Sparse>’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseProduct.h:71:53: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dest&, const Lhs&, const Rhs&, Eigen::SparseShape) [with Dest = Eigen::SparseMatrix; Lhs = Eigen::SparseMatrix; Rhs = Eigen::Transpose >; int ProductType = 8]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseProduct.h:43:11: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dest&, const Lhs&, const Rhs&) [with Dest = Eigen::SparseMatrix; Lhs = Eigen::SparseMatrix; Rhs = Eigen::Transpose >; int ProductType = 8]’ /home/omnipath/local/R/4.5-3.21/RcppEigen/include/Eigen/src/SparseCore/SparseProduct.h:174:51: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::Product&) [with Lhs = Eigen::SparseMatrix; Rhs = Eigen::Transpose >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ CellChat_Rcpp.cpp:20:31: 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] g++ -std=gnu++17 -I"/opt/R-devel/lib/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' -I/usr/local/include -fpic -g -O2 -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/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’ RcppExports.cpp:22:61: 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’ RcppExports.cpp:22:61: 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 -shared -L/usr/local/lib -o CellChat.so CellChat_Rcpp.o RcppExports.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-CellChat/00new/CellChat/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CellChat) Skipping 2 packages ahead of CRAN: RcppArmadillo, spatstat.explore Skipping install of 'CellChat' from a github remote, the SHA1 (e4f68625) has not changed since last install. Use `force = TRUE` to force installation Downloading GitHub repo saezlab/OmnipathR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyUqF9i/remotes13d46e1a5285cc/saezlab-OmnipathR-fe4d2c2/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘OmnipathR/.github’ * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.15.14.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.14’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-05-22 03:22:43] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-05-22 01:22:32 UTC; omnipath [2025-05-22 03:22:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-05-22 03:22:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-22 01:22:33 UTC; unix [2025-05-22 03:22:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.14 [2025-05-22 03:22:43] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-05-22 03:22:43] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-22 03:22:43] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-05-22 03:22:43] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.14(2025-05-22); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-05-22 03:22:43] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-05-22 03:22:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Contains 1 files. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-22 03:22:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:43] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-05-22 01:22:32 UTC; omnipath [2025-05-22 03:22:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-05-22 03:22:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-22 01:22:33 UTC; unix [2025-05-22 03:22:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.14 [2025-05-22 03:22:45] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-05-22 03:22:45] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-22 03:22:45] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-05-22 03:22:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.14(2025-05-22); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-05-22 03:22:45] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-05-22 03:22:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Contains 1 files. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-22 03:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-22 03:22:45] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) Downloading GitHub repo saezlab/decoupleR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyUqF9i/remotes13d46e4b529fc7/saezlab-decoupleR-ee88686/DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION * building ‘decoupleR_2.9.7.tar.gz’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.9.7’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR) [ Finished: 2025-05-22 03:22:52 CEST ]