############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf gINTomics.buildbin-libdir && mkdir gINTomics.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gINTomics_1.3.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gINTomics.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gINTomics.buildbin-libdir gINTomics_1.3.0.tar.gz' >>>>>>> * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.3.0’ ** using staged installation ** R [2025-02-05 00:42:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:42:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:42:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-05 00:42:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04 [2025-02-05 00:42:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:26:57 UTC; unix [2025-02-05 00:42:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-05 00:42:48] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-05 00:42:49] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown)] [2025-02-05 00:42:49] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-05 00:42:49] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-02-05 00:42:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Contains 1 files. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-05 00:42:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-05 00:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-05 00:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-05 00:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-05 00:42:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:42:50] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-02-05 00:43:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-05 00:43:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04 [2025-02-05 00:43:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:26:57 UTC; unix [2025-02-05 00:43:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-05 00:43:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-05 00:43:16] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown)] [2025-02-05 00:43:16] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-05 00:43:16] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-02-05 00:43:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Contains 1 files. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-05 00:43:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-05 00:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-05 00:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-05 00:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-05 00:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:16] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-02-05 00:43:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:53] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-05 00:43:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04 [2025-02-05 00:43:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:26:57 UTC; unix [2025-02-05 00:43:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-05 00:43:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-05 00:43:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown)] [2025-02-05 00:43:53] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-05 00:43:53] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-02-05 00:43:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-05 00:43:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:53] [TRACE] [OmnipathR] Contains 1 files. [2025-02-05 00:43:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-05 00:43:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:43:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-05 00:43:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-05 00:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-05 00:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-05 00:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-05 00:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:43:54] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-05 00:44:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:44:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-05 00:44:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04 [2025-02-05 00:44:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:26:57 UTC; unix [2025-02-05 00:44:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-05 00:44:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-05 00:44:20] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown)] [2025-02-05 00:44:20] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-05 00:44:20] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-02-05 00:44:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Contains 1 files. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-05 00:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-05 00:44:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-05 00:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-05 00:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-05 00:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-05 00:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-05 00:44:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)