Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2152/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TransView 1.49.0 (landing page) Julius Muller
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the TransView package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView |
Version: 1.49.0 |
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.49.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir |
StartedAt: 2024-08-27 02:03:43 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 02:03:51 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 8.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: TransView_1.49.0.tgz |
PackageFileSize: 2.099 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.49.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TransView.buildbin-libdir TransView_1.49.0.tar.gz' >>>>>>> * installing *source* package ‘TransView’ ... ** 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 -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 R_init_TransView.c -o R_init_TransView.o 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 -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 bin_density.c -o bin_density.o 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 construct_dc.c -o construct_dc.o In file included from construct_dc.c:23: In file included from ./parse_sam.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/sam.h:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts.h:36: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes] HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT' #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first))) ^ 1 warning generated. 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 parse_sam.c -o parse_sam.o parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); ~~ ^~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat] warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); ~~ ^~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:23:23: note: expanded from macro 'bam1_cigar' #define bam1_cigar(b) (bam_get_cigar((b))) ^~~~~~~~~~~~~~~~~~~~ parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] printf("Pos %d\n",current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, ^~~~~~~~~~~~~~~~~~~~~~ parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. 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 slice_dc.c -o slice_dc.o 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 visuals.c -o visuals.o 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 TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.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/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/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 (TransView) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR TransView.buildbin-libdir/TransView/libs/TransView.so >>>>>>> >>>>>>> Paths before fix: TransView.buildbin-libdir/TransView/libs/TransView.so: TransView.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/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 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /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" "TransView.buildbin-libdir/TransView/libs/TransView.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so" >>>>>>> Paths after fix: TransView.buildbin-libdir/TransView/libs/TransView.so: TransView.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/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 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)