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This page was generated on 2024-10-15 21:55 -0400 (Tue, 15 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4529
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4479
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 2094/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Structstrings 1.20.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2024-10-13 14:00 -0400 (Sun, 13 Oct 2024)
git_url: https://git.bioconductor.org/packages/Structstrings
git_branch: RELEASE_3_19
git_last_commit: 18cf3f2
git_last_commit_date: 2024-04-30 11:13:11 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for Structstrings on kjohnson1

To the developers/maintainers of the Structstrings package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Structstrings.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: Structstrings
Version: 1.20.0
Command: rm -rf Structstrings.buildbin-libdir && mkdir Structstrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Structstrings_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Structstrings.buildbin-libdir
StartedAt: 2024-10-15 20:31:24 -0400 (Tue, 15 Oct 2024)
EndedAt: 2024-10-15 20:31:52 -0400 (Tue, 15 Oct 2024)
EllapsedTime: 28.1 seconds
RetCode: 0
Status:   OK  
PackageFile: Structstrings_1.20.0.tgz
PackageFileSize: 808.8 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Structstrings.buildbin-libdir && mkdir Structstrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Structstrings_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Structstrings.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Structstrings.buildbin-libdir Structstrings_1.20.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Structstrings’ ...
** using staged installation
** libs
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  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DotBracketDataFrame_class.c -o DotBracketDataFrame_class.o
DotBracketDataFrame_class.c:40:70: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
        error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close);
                           ~~                                        ^~~~~~~~~~~~
                           %c
DotBracketDataFrame_class.c:40:84: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
        error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close);
                             ~~                                                    ^~~~~~~~~~~~~
                             %c
DotBracketDataFrame_class.c:52:66: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
    error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open,  bracket_close);
                       ~~                                        ^~~~~~~~~~~~
                       %c
DotBracketDataFrame_class.c:52:81: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
    error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open,  bracket_close);
                         ~~                                                     ^~~~~~~~~~~~~
                         %c
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Structstrings.c -o R_init_Structstrings.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.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 Structstrings.so DotBracketDataFrame_class.o IRanges_stubs.o R_init_Structstrings.o S4Vectors_stubs.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/Structstrings.buildbin-libdir/00LOCK-Structstrings/00new/Structstrings/libs
** R
** data
** 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 (Structstrings)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so
>>>>>>> 

>>>>>>> Paths before fix:
Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so:
	Structstrings.so (compatibility version 0.0.0, current version 0.0.0)
	/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" "Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so"

>>>>>>> Paths after fix:
Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.so:
	Structstrings.so (compatibility version 0.0.0, current version 0.0.0)
	/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)