Wolfgang Kaisers
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/seqTools |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1de1371 |
| git_last_commit_date: 2024-04-30 10:40:35 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:45 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1950/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqTools 1.38.0 (landing page) Wolfgang Kaisers
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the seqTools package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: seqTools |
| Version: 1.38.0 |
| Command: rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqTools_1.38.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R seqTools.buildbin-libdir |
| StartedAt: 2024-05-07 02:56:39 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 02:56:42 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 3.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: seqTools_1.38.0.tgz |
| PackageFileSize: 814.7 KiB |
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### Running command:
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### rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqTools_1.38.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R seqTools.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqTools.buildbin-libdir seqTools_1.38.0.tar.gz'
>>>>>>>
* installing *source* package ‘seqTools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seqTools.c -o seqTools.o
seqTools.c:851:65: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
error("[count_genome_Kmers] character mismatch at position %u!");
~^
seqTools.c:3296:71: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale);
~~ ^~~~~
%f
seqTools.c:3306:75: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale);
~~ ^~~~~
%f
3 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/seqTools.buildbin-libdir/00LOCK-seqTools/00new/seqTools/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 (seqTools)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR seqTools.buildbin-libdir/seqTools/libs/seqTools.so
>>>>>>>
>>>>>>> Paths before fix:
seqTools.buildbin-libdir/seqTools/libs/seqTools.so:
seqTools.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"
>>>>>>> Paths after fix:
seqTools.buildbin-libdir/seqTools/libs/seqTools.so:
seqTools.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)