Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 679/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
esATAC 1.26.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
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 esATAC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esATAC.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: esATAC |
Version: 1.26.0 |
Command: rm -rf esATAC.buildbin-libdir && mkdir esATAC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh esATAC_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R esATAC.buildbin-libdir |
StartedAt: 2024-06-11 11:09:24 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 11:12:55 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 211.5 seconds |
RetCode: 0 |
Status: OK |
PackageFile: esATAC_1.26.0.tgz |
PackageFileSize: 8.159 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf esATAC.buildbin-libdir && mkdir esATAC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh esATAC_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R esATAC.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=esATAC.buildbin-libdir esATAC_1.26.0.tar.gz' >>>>>>> * installing *source* package ‘esATAC’ ... ** 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 -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedLine.cpp -o BedLine.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedUtils.cpp -o BedUtils.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChrDivi.cpp -o ChrDivi.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutCountPre.cpp -o CutCountPre.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutSiteCount.cpp -o CutSiteCount.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibComplexQC.cpp -o LibComplexQC.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SortBed.cpp -o SortBed.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_wrapper.cpp -o rcpp_wrapper.o rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable] int tmp_k; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c renamer.cpp -o renamer.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.cc -o sam2bed.o sam2bed.cc:125:16: warning: unused variable 'xspm' [-Wunused-variable] regmatch_t xspm[1]; ^ sam2bed.cc:294:16: warning: unused variable 'xspm' [-Wunused-variable] regmatch_t xspm[1]; ^ 2 warnings generated. 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 esATAC.so BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/esATAC.buildbin-libdir/00LOCK-esATAC/00new/esATAC/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 (esATAC) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR esATAC.buildbin-libdir/esATAC/libs/esATAC.so >>>>>>> >>>>>>> Paths before fix: esATAC.buildbin-libdir/esATAC/libs/esATAC.so: esATAC.so (compatibility version 0.0.0, current version 0.0.0) /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) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "esATAC.buildbin-libdir/esATAC/libs/esATAC.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "esATAC.buildbin-libdir/esATAC/libs/esATAC.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "esATAC.buildbin-libdir/esATAC/libs/esATAC.so" >>>>>>> Paths after fix: esATAC.buildbin-libdir/esATAC/libs/esATAC.so: esATAC.so (compatibility version 0.0.0, current version 0.0.0) /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) /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)