Ji-Ping Wang
| Snapshot Date: 2024-11-25 13:40 -0500 (Mon, 25 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/DegNorm |
| git_branch: devel |
| git_last_commit: 3be95e6 |
| git_last_commit_date: 2024-10-29 10:47:31 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-26 11:44 -0500 (Tue, 26 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4350 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4108 |
| 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 521/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DegNorm 1.17.0 (landing page) Ji-Ping Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the DegNorm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DegNorm.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: DegNorm |
| Version: 1.17.0 |
| Command: rm -rf DegNorm.buildbin-libdir && mkdir DegNorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DegNorm_1.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DegNorm.buildbin-libdir |
| StartedAt: 2024-11-26 07:28:35 -0500 (Tue, 26 Nov 2024) |
| EndedAt: 2024-11-26 07:28:57 -0500 (Tue, 26 Nov 2024) |
| EllapsedTime: 21.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: DegNorm_1.17.0.tgz |
| PackageFileSize: 3.244 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DegNorm.buildbin-libdir && mkdir DegNorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DegNorm_1.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DegNorm.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DegNorm.buildbin-libdir DegNorm_1.17.0.tar.gz' >>>>>>> * installing *source* package ‘DegNorm’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c degnormCPP.cpp -o degnormCPP.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DegNorm.so RcppExports.o degnormCPP.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/DegNorm.buildbin-libdir/00LOCK-DegNorm/00new/DegNorm/libs ** R ** data ** 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 (DegNorm) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so >>>>>>> >>>>>>> Paths before fix: DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so: DegNorm.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so" >>>>>>> Paths after fix: DegNorm.buildbin-libdir/DegNorm/libs/DegNorm.so: DegNorm.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)