[ Started: 2023-06-12 22:50:11 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/BiocManager_1.30.21.tar.gz'
Content type 'application/x-gzip' length 582625 bytes (568 KB)
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trying URL 'https://cran.uni-muenster.de/src/contrib/broom_1.0.5.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/bslib_0.5.0.tar.gz'
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downloaded 4.7 MB

trying URL 'https://cran.uni-muenster.de/src/contrib/curl_5.0.1.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/gargle_1.5.0.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/ggrastr_1.0.2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/googledrive_2.1.1.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/googlesheets4_1.1.1.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/jsonlite_1.8.5.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/locfit_1.5-9.8.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/matrixStats_1.0.0.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/plotly_4.10.2.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/reticulate_1.30.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/rmarkdown_2.22.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/sp_1.6-1.tar.gz'
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trying URL 'https://cran.uni-muenster.de/src/contrib/usethis_2.2.0.tar.gz'
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* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ 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 (BiocManager)
* installing *source* package ‘broom’ ...
** package ‘broom’ 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 (broom)
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/local/include
Using PKG_LIBS=-L/usr/local/lib -lcurl
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c callbacks.c -o callbacks.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c curl.c -o curl.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c download.c -o download.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c escape.c -o escape.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c fetch.c -o fetch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c form.c -o form.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c getdate.c -o getdate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c handle.c -o handle.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ieproxy.c -o ieproxy.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c interrupt.c -o interrupt.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c multi.c -o multi.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nslookup.c -o nslookup.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c options.c -o options.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c reflist.c -o reflist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c split.c -o split.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ssl.c -o ssl.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c typechecking.c -o typechecking.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c version.c -o version.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c winidn.c -o winidn.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c writer.c -o writer.o
gcc -shared -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -L/usr/local/lib -lcurl
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-curl/00new/curl/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 (curl)
* installing *source* package ‘ggrastr’ ...
** package ‘ggrastr’ 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 (ggrastr)
* 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 ‘locfit’ ...
** package ‘locfit’ 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 -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c S_enter.c -o S_enter.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c band.c -o band.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dbinom.c -o dbinom.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dens_haz.c -o dens_haz.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dens_int.c -o dens_int.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dens_odi.c -o dens_odi.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c density.c -o density.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_atree.c -o ev_atree.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_interp.c -o ev_interp.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_kdtre.c -o ev_kdtre.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_main.c -o ev_main.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_sphere.c -o ev_sphere.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ev_trian.c -o ev_trian.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c family.c -o family.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c fitted.c -o fitted.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c frend.c -o frend.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_adap.c -o lf_adap.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_dercor.c -o lf_dercor.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_fitfun.c -o lf_fitfun.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_nbhd.c -o lf_nbhd.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_robust.c -o lf_robust.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_vari.c -o lf_vari.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lf_wdiag.c -o lf_wdiag.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lfstr.c -o lfstr.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c locfit.c -o locfit.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_chol.c -o m_chol.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_eigen.c -o m_eigen.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_icirc.c -o m_icirc.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_imont.c -o m_imont.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_isimp.c -o m_isimp.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_isphr.c -o m_isphr.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_jacob.c -o m_jacob.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_max.c -o m_max.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_qr.c -o m_qr.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_solve.c -o m_solve.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_svd.c -o m_svd.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c m_vector.c -o m_vector.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c math.c -o math.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c minmax.c -o minmax.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c pcomp.c -o pcomp.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c preplot.c -o preplot.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c prob.c -o prob.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c procv.c -o procv.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scb.c -o scb.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scb_cons.c -o scb_cons.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scb_crit.c -o scb_crit.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scb_iface.c -o scb_iface.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c simul.c -o simul.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c smisc.c -o smisc.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c startlf.c -o startlf.o
gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c weight.c -o weight.o
gcc -std=gnu17 -shared -L/usr/local/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-locfit/00new/locfit/libs
** R
** data
** 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 (locfit)
* installing *source* package ‘matrixStats’ ...
** package ‘matrixStats’ 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 000.init.c -o 000.init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c allocMatrix2.c -o allocMatrix2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c binCounts.c -o binCounts.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c binMeans.c -o binMeans.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c colCounts.c -o colCounts.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c colOrderStats.c -o colOrderStats.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c colRanges.c -o colRanges.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c diff2.c -o diff2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c indexByRow.c -o indexByRow.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c logSumExp.c -o logSumExp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c mean2.c -o mean2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c naming.c -o naming.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c productExpSumLog.c -o productExpSumLog.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c psortKM.c -o psortKM.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowCounts.c -o rowCounts.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowCummaxs.c -o rowCummaxs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowCummins.c -o rowCummins.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowCumprods.c -o rowCumprods.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowCumsums.c -o rowCumsums.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowDiffs.c -o rowDiffs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowLogSumExp.c -o rowLogSumExp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowMads.c -o rowMads.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowMeans2.c -o rowMeans2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowMedians.c -o rowMedians.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowOrderStats.c -o rowOrderStats.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowRanges.c -o rowRanges.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowRanksWithTies.c -o rowRanksWithTies.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowSums2.c -o rowSums2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rowVars.c -o rowVars.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c signTabulate.c -o signTabulate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c sum2.c -o sum2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c validateIndices.c -o validateIndices.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c weightedMean.c -o weightedMean.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c weightedMedian.c -o weightedMedian.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c x_OP_y.c -o x_OP_y.o
gcc -shared -L/usr/local/lib -o matrixStats.so 000.init.o allocMatrix2.o anyMissing.o binCounts.o binMeans.o colCounts.o colOrderStats.o colRanges.o diff2.o indexByRow.o logSumExp.o mean2.o naming.o productExpSumLog.o psortKM.o rowCounts.o rowCummaxs.o rowCummins.o rowCumprods.o rowCumsums.o rowDiffs.o rowLogSumExp.o rowMads.o rowMeans2.o rowMedians.o rowOrderStats.o rowRanges.o rowRanksWithTies.o rowSums2.o rowVars.o signTabulate.o sum2.o validateIndices.o weightedMean.o weightedMedian.o x_OP_y.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-matrixStats/00new/matrixStats/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 (matrixStats)
* installing *source* package ‘sp’ ...
** package ‘sp’ 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 Rcentroid.c -o Rcentroid.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c gcdist.c -o gcdist.o
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 pip.c -o pip.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c pip2.c -o pip2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c sp_xports.c -o sp_xports.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c surfaceArea.c -o surfaceArea.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c zerodist.c -o zerodist.o
gcc -shared -L/usr/local/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-sp/00new/sp/libs
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** installing vignettes
** testing if installed package can be loaded from temporary location
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* DONE (sp)
* installing *source* package ‘bslib’ ...
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* installing *source* package ‘gargle’ ...
** package ‘gargle’ successfully unpacked and MD5 sums checked
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* installing *source* package ‘plotly’ ...
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* DONE (plotly)
* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ successfully unpacked and MD5 sums checked
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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/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'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c event_loop.cpp -o event_loop.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/usr/local/include    -fpic  -g -O2  -c libpython.cpp -o libpython.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/usr/local/include    -fpic  -g -O2  -c output.cpp -o output.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/usr/local/include    -fpic  -g -O2  -c python.cpp -o python.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/usr/local/include    -fpic  -g -O2  -c readline.cpp -o readline.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/usr/local/include    -fpic  -g -O2  -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-reticulate/00new/reticulate/libs
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** inst
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*** installing help indices
*** copying figures
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** installing vignettes
** testing if installed package can be loaded from temporary location
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* installing *source* package ‘googlesheets4’ ...
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* DONE (googlesheets4)

The downloaded source packages are in
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Bioconductor version 3.17 (BiocManager 1.30.21), R 4.3.0 (2023-04-21)
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* installing *source* package ‘biomaRt’ ...
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*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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* DONE (biomaRt)
* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++14
g++ -std=gnu++14 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c densne.cpp -o densne.o
g++ -std=gnu++14 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c densvis.cpp -o densvis.o
g++ -std=gnu++14 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c sptree.cpp -o sptree.o
g++ -std=gnu++14 -shared -L/usr/local/lib -o densvis.so RcppExports.o densne.o densvis.o sptree.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
installing to /home/omnipath/local/R/4.3-3.17/densvis/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
* DONE (densvis)
* installing *source* package ‘limma’ ...
** 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 normexp.c -o normexp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-limma/00new/limma/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 (limma)
* installing *source* package ‘MatrixGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’
** 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 (MatrixGenerics)
* installing *source* package ‘scattermore’ ...
** package ‘scattermore’ 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/usr/local/include    -fpic  -g -O2  -c histogram_to_rgbwt.cpp -o histogram_to_rgbwt.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c kernel_histogram.cpp -o kernel_histogram.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c kernel_rgbwt.cpp -o kernel_rgbwt.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_histogram.cpp -o scatter_histogram.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_indexed_rgbwt.cpp -o scatter_indexed_rgbwt.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_lines_histogram.cpp -o scatter_lines_histogram.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_lines_rgbwt.cpp -o scatter_lines_rgbwt.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_multicolor_rgbwt.cpp -o scatter_multicolor_rgbwt.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scatter_singlecolor_rgbwt.cpp -o scatter_singlecolor_rgbwt.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c scattermore.c -o scattermore.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o scattermore.so histogram_to_rgbwt.o kernel_histogram.o kernel_rgbwt.o scatter_histogram.o scatter_indexed_rgbwt.o scatter_lines_histogram.o scatter_lines_rgbwt.o scatter_multicolor_rgbwt.o scatter_singlecolor_rgbwt.o scattermore.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-scattermore/00new/scattermore/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 (scattermore)
* installing *source* package ‘DelayedMatrixStats’ ...
** 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 (DelayedMatrixStats)
* installing *source* package ‘edgeR’ ...
** 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'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_add_prior_count.cpp -o R_add_prior_count.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/usr/local/include    -fpic  -g -O2  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.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/usr/local/include    -fpic  -g -O2  -c R_calculate_cpm.cpp -o R_calculate_cpm.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/usr/local/include    -fpic  -g -O2  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.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/usr/local/include    -fpic  -g -O2  -c R_compute_apl.cpp -o R_compute_apl.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/usr/local/include    -fpic  -g -O2  -c R_compute_nbdev.cpp -o R_compute_nbdev.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/usr/local/include    -fpic  -g -O2  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.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/usr/local/include    -fpic  -g -O2  -c R_fit_levenberg.cpp -o R_fit_levenberg.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/usr/local/include    -fpic  -g -O2  -c R_fit_one_group.cpp -o R_fit_one_group.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/usr/local/include    -fpic  -g -O2  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.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/usr/local/include    -fpic  -g -O2  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.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/usr/local/include    -fpic  -g -O2  -c R_loess_by_col.cpp -o R_loess_by_col.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/usr/local/include    -fpic  -g -O2  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
gcc -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 R_process_hairpin_reads.c -o R_process_hairpin_reads.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/usr/local/include    -fpic  -g -O2  -c R_simple_good_turing.cpp -o R_simple_good_turing.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/usr/local/include    -fpic  -g -O2  -c add_prior.cpp -o add_prior.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/usr/local/include    -fpic  -g -O2  -c adj_coxreid.cpp -o adj_coxreid.o
gcc -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 fmm_spline.c -o fmm_spline.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/usr/local/include    -fpic  -g -O2  -c glm_levenberg.cpp -o glm_levenberg.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/usr/local/include    -fpic  -g -O2  -c glm_one_group.cpp -o glm_one_group.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/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.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/usr/local/include    -fpic  -g -O2  -c interpolator.cpp -o interpolator.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/usr/local/include    -fpic  -g -O2  -c nbdev.cpp -o nbdev.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/usr/local/include    -fpic  -g -O2  -c objects.cpp -o objects.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-edgeR/00new/edgeR/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 (edgeR)
* installing *source* package ‘SummarizedExperiment’ ...
** 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 (SummarizedExperiment)
* 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/Rtmp9zmOXF/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: 2023-06-12 22:55:08 CEST ]