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This page was generated on 2024-03-29 11:38:21 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 2167/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.46.0  (landing page)
Julius Muller
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: RELEASE_3_18
git_last_commit: 2a55784
git_last_commit_date: 2023-10-24 09:51:41 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for TransView on merida1


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.

raw results

Summary

Package: TransView
Version: 1.46.0
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir
StartedAt: 2024-03-28 12:36:06 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 12:36:47 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 41.5 seconds
RetCode: 0
Status:   OK  
PackageFile: TransView_1.46.0.tgz
PackageFileSize: 2.11 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.46.0.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_1.46.0.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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/sam.h:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/hts.h:36:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-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/4.3-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
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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-3.18-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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/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/4.3-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/4.3-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/4.3-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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/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)