[ Started: 2023-07-03 23:18:35 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
trying URL 'https://cran.uni-muenster.de/src/contrib/cpp11_0.4.4.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/digest_0.6.32.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/downlit_0.4.3.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/future_1.33.0.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/haven_2.5.3.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/jsonlite_1.8.7.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/pbapply_1.7-2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/pkgbuild_1.4.2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/processx_3.8.2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/RcppAnnoy_0.0.21.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/rmarkdown_2.23.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/spatstat.sparse_3.0-2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/uwot_0.1.16.tar.gz'
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* installing *source* package ‘cpp11’ ...
** package ‘cpp11’ 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 (cpp11)
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c SpookyV2.cpp -o SpookyV2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c aes.c -o aes.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c blake3.c -o blake3.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c blake3_dispatch.c -o blake3_dispatch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c blake3_portable.c -o blake3_portable.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c crc32.c -o crc32.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c crc32c.cpp -o crc32c.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c crc32c_portable.cpp -o crc32c_portable.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c digest.c -o digest.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c digest2int.c -o digest2int.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c md5.c -o md5.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c pmurhash.c -o pmurhash.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c raes.c -o raes.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c sha1.c -o sha1.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c sha2.c -o sha2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c sha256.c -o sha256.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c spooky_serialize.cpp -o spooky_serialize.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I.  -I/usr/local/include    -fpic  -g -O2  -c xxhash.c -o xxhash.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o digest.so SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o crc32c.o crc32c_portable.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-digest/00new/digest/libs
** R
** demo
** 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 (digest)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_array.c -o collapse_array.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_object.c -o collapse_object.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c escape_chars.c -o escape_chars.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_datelist.c -o is_datelist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_recordlist.c -o is_recordlist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c null_to_na.c -o null_to_na.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c num_to_char.c -o num_to_char.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c parse.c -o parse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c prettify.c -o prettify.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c push_parser.c -o push_parser.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c r-base64.c -o r-base64.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c register.c -o register.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c row_collapse.c -o row_collapse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c transpose_list.c -o transpose_list.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c validate.c -o validate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
** 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 (jsonlite)
* installing *source* package ‘pbapply’ ...
** package ‘pbapply’ 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 (pbapply)
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -g -O2  -L/usr/local/lib -Wall tools/px.c -o tools/px
gcc -g -O2  -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock
gcc -g -O2  -L/usr/local/lib supervisor/supervisor.c \
      supervisor/utils.c -o supervisor/supervisor
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c client.c -o client.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c errors.c -o errors.o
gcc -shared  -L/usr/local/lib -o client.so base64.o client.o errors.o  \
	 
if [ -n "" ]; then \
    echo Removing libR.so dependency from client.so; \
    patchelf --remove-needed libR.so client.so; \
fi
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c poll.c -o poll.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c processx-connection.c -o processx-connection.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c processx-vector.c -o processx-vector.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c create-time.c -o create-time.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/childlist.c -o unix/childlist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/connection.c -o unix/connection.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/processx.c -o unix/processx.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/sigchld.c -o unix/sigchld.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/utils.c -o unix/utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/named_pipe.c -o unix/named_pipe.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c cleancall.c -o cleancall.o
gcc -shared -L/usr/local/lib -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o
installing via 'install.libs.R' to /home/omnipath/local/R/4.3-3.17/00LOCK-processx/00new/processx
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (processx)
* installing *source* package ‘RcppAnnoy’ ...
** package ‘RcppAnnoy’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c annoy.cpp -o annoy.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c arch.cpp -o arch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c version.cpp -o version.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o RcppAnnoy.so RcppExports.o annoy.o arch.o init.o version.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-RcppAnnoy/00new/RcppAnnoy/libs
** R
** demo
** 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 (RcppAnnoy)
* installing *source* package ‘spatstat.sparse’ ...
** package ‘spatstat.sparse’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c linalg.c -o linalg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c sparselinalg.c -o sparselinalg.o
gcc -shared -L/usr/local/lib -o spatstat.sparse.so init.o linalg.o sparselinalg.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-spatstat.sparse/00new/spatstat.sparse/libs
** 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
** 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 (spatstat.sparse)
* installing *source* package ‘downlit’ ...
** package ‘downlit’ 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 (downlit)
* installing *source* package ‘future’ ...
** package ‘future’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (future)
* installing *source* package ‘haven’ ...
** package ‘haven’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lz
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c tagged_na.c -o tagged_na.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/CKHashTable.c -o readstat/CKHashTable.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_bits.c -o readstat/readstat_bits.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_convert.c -o readstat/readstat_convert.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_error.c -o readstat/readstat_error.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_io_unistd.c -o readstat/readstat_io_unistd.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_malloc.c -o readstat/readstat_malloc.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_metadata.c -o readstat/readstat_metadata.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_parser.c -o readstat/readstat_parser.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_value.c -o readstat/readstat_value.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_variable.c -o readstat/readstat_variable.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_writer.c -o readstat/readstat_writer.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/ieee.c -o readstat/sas/ieee.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas.c -o readstat/sas/readstat_sas.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bcat_read.c -o readstat/sas/readstat_sas7bcat_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bcat_write.c -o readstat/sas/readstat_sas7bcat_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bdat_read.c -o readstat/sas/readstat_sas7bdat_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bdat_write.c -o readstat/sas/readstat_sas7bdat_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas_rle.c -o readstat/sas/readstat_sas_rle.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport.c -o readstat/sas/readstat_xport.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport_parse_format.c -o readstat/sas/readstat_xport_parse_format.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport_read.c -o readstat/sas/readstat_xport_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport_write.c -o readstat/sas/readstat_xport_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por.c -o readstat/spss/readstat_por.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_parse.c -o readstat/spss/readstat_por_parse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_read.c -o readstat/spss/readstat_por_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_write.c -o readstat/spss/readstat_por_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav.c -o readstat/spss/readstat_sav.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_compress.c -o readstat/spss/readstat_sav_compress.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_parse.c -o readstat/spss/readstat_sav_parse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_parse_timestamp.c -o readstat/spss/readstat_sav_parse_timestamp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_read.c -o readstat/spss/readstat_sav_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_write.c -o readstat/spss/readstat_sav_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_spss.c -o readstat/spss/readstat_spss.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_spss_parse.c -o readstat/spss/readstat_spss_parse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_compress.c -o readstat/spss/readstat_zsav_compress.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_read.c -o readstat/spss/readstat_zsav_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_write.c -o readstat/spss/readstat_zsav_write.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta.c -o readstat/stata/readstat_dta.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_parse_timestamp.c -o readstat/stata/readstat_dta_parse_timestamp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_read.c -o readstat/stata/readstat_dta_read.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_write.c -o readstat/stata/readstat_dta_write.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c DfReader.cpp -o DfReader.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c DfWriter.cpp -o DfWriter.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include   -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c haven_types.cpp -o haven_types.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o haven.so tagged_na.o readstat/CKHashTable.o readstat/readstat_bits.o readstat/readstat_convert.o readstat/readstat_error.o readstat/readstat_io_unistd.o readstat/readstat_malloc.o readstat/readstat_metadata.o readstat/readstat_parser.o readstat/readstat_value.o readstat/readstat_variable.o readstat/readstat_writer.o readstat/sas/ieee.o readstat/sas/readstat_sas.o readstat/sas/readstat_sas7bcat_read.o readstat/sas/readstat_sas7bcat_write.o readstat/sas/readstat_sas7bdat_read.o readstat/sas/readstat_sas7bdat_write.o readstat/sas/readstat_sas_rle.o readstat/sas/readstat_xport.o readstat/sas/readstat_xport_parse_format.o readstat/sas/readstat_xport_read.o readstat/sas/readstat_xport_write.o readstat/spss/readstat_por.o readstat/spss/readstat_por_parse.o readstat/spss/readstat_por_read.o readstat/spss/readstat_por_write.o readstat/spss/readstat_sav.o readstat/spss/readstat_sav_compress.o readstat/spss/readstat_sav_parse.o readstat/spss/readstat_sav_parse_timestamp.o readstat/spss/readstat_sav_read.o readstat/spss/readstat_sav_write.o readstat/spss/readstat_spss.o readstat/spss/readstat_spss_parse.o readstat/spss/readstat_zsav_compress.o readstat/spss/readstat_zsav_read.o readstat/spss/readstat_zsav_write.o readstat/stata/readstat_dta.o readstat/stata/readstat_dta_parse_timestamp.o readstat/stata/readstat_dta_read.o readstat/stata/readstat_dta_write.o DfReader.o DfWriter.o cpp11.o haven_types.o -lz
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-haven/00new/haven/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 (haven)
* installing *source* package ‘pkgbuild’ ...
** package ‘pkgbuild’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 (pkgbuild)
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** 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 (rmarkdown)
* installing *source* package ‘uwot’ ...
** package ‘uwot’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c connected_components.cpp -o connected_components.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c nn_parallel.cpp -o nn_parallel.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c perplexity.cpp -o perplexity.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c r_uwot.cpp -o r_uwot.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c smooth_knn.cpp -o smooth_knn.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c supervised.cpp -o supervised.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c thread.cpp -o thread.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppProgress/include' -I'/home/omnipath/local/R/4.3-3.17/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.17/dqrng/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2  -c transform.cpp -o transform.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o uwot.so RcppExports.o connected_components.o nn_parallel.o perplexity.o r_uwot.o smooth_knn.o supervised.o thread.o transform.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-uwot/00new/uwot/libs
** 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
** 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 (uwot)

The downloaded source packages are in
	‘/tmp/Rtmp0BNBro/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.21), R 4.3.0 (2023-04-21)
Old packages: 'AnnotationDbi', 'DelayedArray', 'DESeq2', 'GSVA',
  'sparseMatrixStats'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/DelayedArray_0.26.6.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/DESeq2_1.40.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GSVA_1.48.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/sparseMatrixStats_1.12.2.tar.gz'
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* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** 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 (AnnotationDbi)
* installing *source* package ‘DelayedArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c compress_atomic_vector.c -o compress_atomic_vector.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o sparseMatrix_utils.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘sweep’ in package ‘DelayedArray’
Creating a new generic function for ‘scale’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
** 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 (DelayedArray)
* installing *source* package ‘DESeq2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-DESeq2/00new/DESeq2/libs
** 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
** 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 (DESeq2)
* installing *source* package ‘sparseMatrixStats’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c SparseMatrixView.cpp -o SparseMatrixView.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c methods.cpp -o methods.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c row_methods.cpp -o row_methods.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-sparseMatrixStats/00new/sparseMatrixStats/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 (sparseMatrixStats)
* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ks_test.c -o ks_test.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-GSVA/00new/GSVA/libs
** 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
** 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 (GSVA)

The downloaded source packages are in
	‘/tmp/Rtmp0BNBro/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.21), R 4.3.0 (2023-04-21)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2023-07-03 23:23:01 CEST ]