| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 2094/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Structstrings 1.20.0 (landing page) Felix G.M. Ernst
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | 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 | | ||||||||
|
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. |
| 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: 2024-06-10 00:42:31 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:43:00 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 28.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Structstrings_1.20.0.tgz |
| PackageFileSize: 809.4 KiB |
##############################################################################
##############################################################################
###
### 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 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 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Structstrings.c -o R_init_Structstrings.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.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 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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/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" "Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.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" "Structstrings.buildbin-libdir/Structstrings/libs/Structstrings.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" "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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/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)