[ Started: 2025-02-20 00:05:09 CET ]
[ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.21"
[3] "/home/omnipath/local/R/4.5"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
Old packages: 'curl', 'jsonlite', 'relations', 'tinytex', 'wppi', 'xfun'
trying URL 'https://cloud.r-project.org/src/contrib/curl_6.2.1.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.9.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/relations_0.6-15.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/tinytex_0.55.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.51.tar.gz'
* installing *source* package ‘curl’ ...
** this is package ‘curl’ version ‘6.2.1’
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu 
Using PKG_LIBS=-lcurl 
Found recent recent version of libcurl
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
rm -f curl.so callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.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 urlparser.o utils.o version.o winidn.o writer.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c dryrun.c -o dryrun.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c findport.c -o findport.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c urlparser.c -o urlparser.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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/include/x86_64-linux-gnu  -DSTRICT_R_HEADERS -DR_NO_REMAP  -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 dryrun.o escape.o fetch.o findport.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 urlparser.o utils.o version.o winidn.o writer.o -lcurl
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-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 ‘jsonlite’ ...
** this is package ‘jsonlite’ version ‘1.9.0’
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -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/4.5-3.21/00LOCK-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 ‘relations’ ...
** this is package ‘relations’ version ‘0.6-15’
** package ‘relations’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (relations)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.15.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-19 00:15:29 UTC; omnipath
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-19 00:15:30 UTC; unix
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-20 00:05:30] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-20; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-20 00:05:30] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-20 00:05:30] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:30] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-19 00:15:29 UTC; omnipath
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-19 00:15:30 UTC; unix
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-20 00:05:33] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-20; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-20 00:05:33] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-20 00:05:33] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:33] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-19 00:15:29 UTC; omnipath
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-19 00:15:30 UTC; unix
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-20 00:05:35] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-20; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-20 00:05:35] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-20 00:05:35] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-20 00:05:35] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)
* installing *source* package ‘xfun’ ...
** this is package ‘xfun’ version ‘0.51’
** package ‘xfun’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -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 init.c -o init.o
gcc -shared -L/usr/local/lib -o xfun.so base64.o init.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-xfun/00new/xfun/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 (xfun)
* installing *source* package ‘tinytex’ ...
** this is package ‘tinytex’ version ‘0.55’
** package ‘tinytex’ 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 (tinytex)

The downloaded source packages are in
	‘/tmp/RtmpJV8Lw8/downloaded_packages’
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 4 packages ahead of CRAN: xfun, jsonlite, curl, tinytex
[ Finished: 2025-02-20 00:05:43 CET ]