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This page was generated on 2023-04-12 11:06:30 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD BIN results for TransView on lconway


To the developers/maintainers of the TransView package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2082/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.42.0  (landing page)
Julius Muller
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: RELEASE_3_16
git_last_commit: a2ee720
git_last_commit_date: 2022-11-01 11:07:31 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TransView
Version: 1.42.0
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir
StartedAt: 2023-04-11 00:09:22 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:09:46 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 24.0 seconds
RetCode: 0
Status:   OK  
PackageFile: TransView_1.42.0.tgz
PackageFileSize: 2.054 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.42.0.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_1.42.0.tar.gz'
>>>>>>> 

* installing *source* package ‘TransView’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_TransView.c -o R_init_TransView.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bin_density.c -o bin_density.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -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/4.2/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/sam.h:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/hts.h:36:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/hts_log.h:75:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes]
HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);
^
/Library/Frameworks/R.framework/Versions/4.2/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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c parse_sam.c -o parse_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c slice_dc.c -o slice_dc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c visuals.c -o visuals.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-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 LINKS FOR TransView.buildbin-libdir/TransView/libs/TransView.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so"