Julius Muller
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/TransView |
| git_branch: RELEASE_3_20 |
| git_last_commit: 21d33cd |
| git_last_commit_date: 2024-12-12 03:54:15 -0500 (Thu, 12 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
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 2185/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TransView 1.50.0 (landing page) Julius Muller
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| 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 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: 1.50.0 |
| Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir |
| StartedAt: 2024-12-20 13:38:39 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 13:39:40 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 60.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: TransView_1.50.0.tgz |
| PackageFileSize: 2.133 MiB |
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###
### Running command:
###
### rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TransView.buildbin-libdir TransView_1.50.0.tar.gz'
>>>>>>>
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_TransView.c -o R_init_TransView.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bin_density.c -o bin_density.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/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-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/sam.h:33:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts.h:36:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/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-x86_64/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 '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 'long long' [-Wformat]
current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c slice_dc.c -o slice_dc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c visuals.c -o visuals.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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-x86_64/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/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)