Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2271/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
xcms 4.4.0 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.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: xcms |
Version: 4.4.0 |
Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh xcms_4.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R xcms.buildbin-libdir |
StartedAt: 2024-12-21 17:09:05 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 17:11:06 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 121.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: xcms_4.4.0.tgz |
PackageFileSize: 12.07 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh xcms_4.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R xcms.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=xcms.buildbin-libdir xcms_4.4.0.tar.gz' >>>>>>> * installing *source* package ‘xcms’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o In file included from massifquant/Tracker.cpp:8: massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field] double r_val_i; ^ massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field] double p_val_i; ^ massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field] double r_val_m; ^ massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field] double p_val_m; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o In file included from massifquant/DataKeeper.cpp:4: massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field] struct scanBuf * scbuf; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o obiwarp/mat.cpp:137:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ obiwarp/mat.cpp:545:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ obiwarp/mat.cpp:953:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable] float bestscore; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastMatch.c -o fastMatch.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mzROI.c -o mzROI.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xcms.c -o xcms.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binners.c -o binners.o binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable] int idx = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/xcms.buildbin-libdir/00LOCK-xcms/00new/xcms/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘group’ in package ‘xcms’ Creating a new generic function for ‘sigma’ in package ‘xcms’ ** help *** installing help indices *** copying figures ** 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 (xcms) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR xcms.buildbin-libdir/xcms/libs/xcms.so >>>>>>> >>>>>>> Paths before fix: xcms.buildbin-libdir/xcms/libs/xcms.so: xcms.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 4.4.2) /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" "xcms.buildbin-libdir/xcms/libs/xcms.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "xcms.buildbin-libdir/xcms/libs/xcms.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "xcms.buildbin-libdir/xcms/libs/xcms.so" >>>>>>> Paths after fix: xcms.buildbin-libdir/xcms/libs/xcms.so: xcms.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 4.4.2) /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)