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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.15.6’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:16:59 UTC; unix
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-04 15:17:04] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-04; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown)]
[2025-02-04 15:17:04] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-04 15:17:04] [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: aarch64-apple-darwin23.6.0; 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
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:16:59 UTC; unix
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-04 15:17:05] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-04; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown)]
[2025-02-04 15:17:05] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-04 15:17:05] [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: aarch64-apple-darwin23.6.0; 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
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 15:17:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)