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 12:07 -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 932/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
h5vc 2.40.0 (landing page) Paul Theodor Pyl
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the h5vc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/h5vc.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: h5vc |
Version: 2.40.0 |
Command: rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R h5vc.buildbin-libdir |
StartedAt: 2024-12-21 15:11:35 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 15:12:01 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 26.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: h5vc_2.40.0.tgz |
PackageFileSize: 2.06 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R h5vc.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.40.0.tar.gz' >>>>>>> * installing *source* package ‘h5vc’ ... ** 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’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if(p->indel > 0){ ^~~~~~~~~~~~ tallyBAM.cpp:64:16: note: uninitialized use occurs here str += c; ^ tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true }else if(p->indel > 0){ ^~~~~~~~~~~~~~~~ tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning char c; ^ = '\0' tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function] static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) ^ 5 warnings 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 h5vc.so bam_plbuf.o tallyBAM.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/h5vc.buildbin-libdir/00LOCK-h5vc/00new/h5vc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** testing if installed package keeps a record of temporary installation path * DONE (h5vc) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR h5vc.buildbin-libdir/h5vc/libs/h5vc.so >>>>>>> >>>>>>> Paths before fix: h5vc.buildbin-libdir/h5vc/libs/h5vc.so: h5vc.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.3.0) /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 4.4.2) /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" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" >>>>>>> Paths after fix: h5vc.buildbin-libdir/h5vc/libs/h5vc.so: h5vc.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.3.0) /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 4.4.2) /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)