[ Started: 2025-05-15 22:25:10 CEST ]
[ 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: 'spatstat.utils', 'wppi', 'xgboost'
trying URL 'https://cloud.r-project.org/src/contrib/spatstat.utils_3.1-4.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/xgboost_1.7.11.1.tar.gz'
* installing *source* package ‘spatstat.utils’ ...
** this is package ‘spatstat.utils’ version ‘3.1-4’
** package ‘spatstat.utils’ 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 circxseg.c -o circxseg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c distseg.c -o distseg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c fastinterv.c -o fastinterv.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 inxyp.c -o inxyp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c matchindices.c -o matchindices.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c matchpoints.c -o matchpoints.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ply.c -o ply.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c primefax.c -o primefax.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c revcum.c -o revcum.o
gcc -shared -L/usr/local/lib -o spatstat.utils.so circxseg.o distseg.o fastinterv.o init.o inxyp.o matchindices.o matchpoints.o ply.o primefax.o revcum.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-spatstat.utils/00new/spatstat.utils/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.utils)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-14 21:29:43 UTC; unix
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-15 22:25:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-15 22:25:21] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-15; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-15 22:25:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-05-15 22:25:21] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-15 22:25:21] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-15 22:25:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:21] [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
[2025-05-15 22:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-14 21:29:43 UTC; unix
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-15 22:25:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-15 22:25:24] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-15; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-15 22:25:24] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-05-15 22:25:24] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-15 22:25:24] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:24] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-14 21:29:43 UTC; unix
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-15; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-15 22:25:26] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-05-15 22:25:26] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-15 22:25:26] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-15 22:25:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-15 22:25:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-15 22:25:27] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)
* installing *source* package ‘xgboost’ ...
** this is package ‘xgboost’ version ‘1.7.11.1’
** package ‘xgboost’ successfully unpacked and MD5 sums checked
** using staged installation
configure: Checking if/where backtrace is available
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for backtrace in -lexecinfo... no
checking for backtrace... yes
configure: Checking whether fopen64 is available
checking for fopen64... yes
configure: Endian detection
checking endian... 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
Makevars:22: -DXGBOOST_STRICT_R_MODE=1
Makevars:22: -DDMLC_LOG_BEFORE_THROW=0
Makevars:22: -DDMLC_ENABLE_STD_THREAD=1
Makevars:22: -DDMLC_DISABLE_STDIN=1
Makevars:22: -DDMLC_LOG_CUSTOMIZE=1
Makevars:22: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:22: -DRABIT_CUSTOMIZE_MSG_
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
Makevars:22: -DXGBOOST_STRICT_R_MODE=1
Makevars:22: -DDMLC_LOG_BEFORE_THROW=0
Makevars:22: -DDMLC_ENABLE_STD_THREAD=1
Makevars:22: -DDMLC_DISABLE_STDIN=1
Makevars:22: -DDMLC_LOG_CUSTOMIZE=1
Makevars:22: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:22: -DRABIT_CUSTOMIZE_MSG_
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c xgboost_R.cc -o xgboost_R.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c xgboost_custom.cc -o xgboost_custom.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -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./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/metric.cc -o src/metric/metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/elementwise_metric.cc -o src/metric/elementwise_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/multiclass_metric.cc -o src/metric/multiclass_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/rank_metric.cc -o src/metric/rank_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/auc.cc -o src/metric/auc.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/metric/survival_metric.cc -o src/metric/survival_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/objective.cc -o src/objective/objective.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/regression_obj.cc -o src/objective/regression_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/multiclass_obj.cc -o src/objective/multiclass_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/rank_obj.cc -o src/objective/rank_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/hinge.cc -o src/objective/hinge.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/aft_obj.cc -o src/objective/aft_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/objective/adaptive.cc -o src/objective/adaptive.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/gbm/gbm.cc -o src/gbm/gbm.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/gbm/gbtree.cc -o src/gbm/gbtree.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/gbm/gbtree_model.cc -o src/gbm/gbtree_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/gbm/gblinear.cc -o src/gbm/gblinear.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/gbm/gblinear_model.cc -o src/gbm/gblinear_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/simple_dmatrix.cc -o src/data/simple_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/data.cc -o src/data/data.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/sparse_page_raw_format.cc -o src/data/sparse_page_raw_format.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/ellpack_page.cc -o src/data/ellpack_page.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/gradient_index.cc -o src/data/gradient_index.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/gradient_index_page_source.cc -o src/data/gradient_index_page_source.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/gradient_index_format.cc -o src/data/gradient_index_format.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/sparse_page_dmatrix.cc -o src/data/sparse_page_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/proxy_dmatrix.cc -o src/data/proxy_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/data/iterative_dmatrix.cc -o src/data/iterative_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/predictor/predictor.cc -o src/predictor/predictor.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/predictor/cpu_predictor.cc -o src/predictor/cpu_predictor.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/constraints.cc -o src/tree/constraints.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/param.cc -o src/tree/param.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/tree_model.cc -o src/tree/tree_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/tree_updater.cc -o src/tree/tree_updater.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_approx.cc -o src/tree/updater_approx.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_colmaker.cc -o src/tree/updater_colmaker.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_prune.cc -o src/tree/updater_prune.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_quantile_hist.cc -o src/tree/updater_quantile_hist.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_refresh.cc -o src/tree/updater_refresh.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/tree/updater_sync.cc -o src/tree/updater_sync.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/linear/linear_updater.cc -o src/linear/linear_updater.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/linear/updater_coordinate.cc -o src/linear/updater_coordinate.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/linear/updater_shotgun.cc -o src/linear/updater_shotgun.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/learner.cc -o src/learner.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/logging.cc -o src/logging.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/global_config.cc -o src/global_config.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/collective/communicator.cc -o src/collective/communicator.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/collective/socket.cc -o src/collective/socket.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/charconv.cc -o src/common/charconv.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/column_matrix.cc -o src/common/column_matrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/common.cc -o src/common/common.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/hist_util.cc -o src/common/hist_util.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/host_device_vector.cc -o src/common/host_device_vector.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/io.cc -o src/common/io.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/json.cc -o src/common/json.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/numeric.cc -o src/common/numeric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/pseudo_huber.cc -o src/common/pseudo_huber.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/quantile.cc -o src/common/quantile.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/random.cc -o src/common/random.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/survival_util.cc -o src/common/survival_util.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/threading_utils.cc -o src/common/threading_utils.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/timer.cc -o src/common/timer.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/common/version.cc -o src/common/version.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/c_api/c_api.cc -o src/c_api/c_api.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c src/c_api/c_api_error.cc -o src/c_api/c_api_error.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c amalgamation/dmlc-minimum0.cc -o amalgamation/dmlc-minimum0.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c rabit/src/engine.cc -o rabit/src/engine.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c rabit/src/rabit_c_api.cc -o rabit/src/rabit_c_api.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2   -c rabit/src/allreduce_base.cc -o rabit/src/allreduce_base.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./init.o ./src/metric/metric.o ./src/metric/elementwise_metric.o ./src/metric/multiclass_metric.o ./src/metric/rank_metric.o ./src/metric/auc.o ./src/metric/survival_metric.o ./src/objective/objective.o ./src/objective/regression_obj.o ./src/objective/multiclass_obj.o ./src/objective/rank_obj.o ./src/objective/hinge.o ./src/objective/aft_obj.o ./src/objective/adaptive.o ./src/gbm/gbm.o ./src/gbm/gbtree.o ./src/gbm/gbtree_model.o ./src/gbm/gblinear.o ./src/gbm/gblinear_model.o ./src/data/simple_dmatrix.o ./src/data/data.o ./src/data/sparse_page_raw_format.o ./src/data/ellpack_page.o ./src/data/gradient_index.o ./src/data/gradient_index_page_source.o ./src/data/gradient_index_format.o ./src/data/sparse_page_dmatrix.o ./src/data/proxy_dmatrix.o ./src/data/iterative_dmatrix.o ./src/predictor/predictor.o ./src/predictor/cpu_predictor.o ./src/tree/constraints.o ./src/tree/param.o ./src/tree/tree_model.o ./src/tree/tree_updater.o ./src/tree/updater_approx.o ./src/tree/updater_colmaker.o ./src/tree/updater_prune.o ./src/tree/updater_quantile_hist.o ./src/tree/updater_refresh.o ./src/tree/updater_sync.o ./src/linear/linear_updater.o ./src/linear/updater_coordinate.o ./src/linear/updater_shotgun.o ./src/learner.o ./src/logging.o ./src/global_config.o ./src/collective/communicator.o ./src/collective/socket.o ./src/common/charconv.o ./src/common/column_matrix.o ./src/common/common.o ./src/common/hist_util.o ./src/common/host_device_vector.o ./src/common/io.o ./src/common/json.o ./src/common/numeric.o ./src/common/pseudo_huber.o ./src/common/quantile.o ./src/common/random.o ./src/common/survival_util.o ./src/common/threading_utils.o ./src/common/timer.o ./src/common/version.o ./src/c_api/c_api.o ./src/c_api/c_api_error.o ./amalgamation/dmlc-minimum0.o ./rabit/src/engine.o ./rabit/src/rabit_c_api.o ./rabit/src/allreduce_base.o -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-xgboost/00new/xgboost/libs
** R
** data
** 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 (xgboost)

The downloaded source packages are in
	‘/tmp/RtmpWKfGQ2/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' 

[ Finished: 2025-05-15 22:31:19 CEST ]