Mark Robinson
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Repitools |
| git_branch: RELEASE_3_19 |
| git_last_commit: bbf5dba |
| git_last_commit_date: 2024-04-30 10:24:48 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:42 -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 1737/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Repitools 1.50.0 (landing page) Mark Robinson
| 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 Repitools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Repitools.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: Repitools |
| Version: 1.50.0 |
| Command: rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Repitools_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Repitools.buildbin-libdir |
| StartedAt: 2024-06-10 00:34:52 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:35:51 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 58.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Repitools_1.50.0.tgz |
| PackageFileSize: 2.502 MiB |
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### Running command:
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### rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Repitools_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Repitools.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Repitools.buildbin-libdir Repitools_1.50.0.tar.gz'
>>>>>>>
* installing *source* package ‘Repitools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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/opt/R/x86_64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c const.c -o const.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c hyp2f1.c -o hyp2f1.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp:33:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
int * x, nval, hs, is, i;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c mtherr.c -o mtherr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c ringo_stuff.c -o ringo_stuff.o
ringo_stuff.c:13:24: warning: unused variable 'Ringo_calls' [-Wunused-variable]
static R_CallMethodDef Ringo_calls[] = {
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Repitools.so const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/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 (Repitools)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Repitools.buildbin-libdir/Repitools/libs/Repitools.so
>>>>>>>
>>>>>>> Paths before fix:
Repitools.buildbin-libdir/Repitools/libs/Repitools.so:
Repitools.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/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" "Repitools.buildbin-libdir/Repitools/libs/Repitools.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" "Repitools.buildbin-libdir/Repitools/libs/Repitools.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" "Repitools.buildbin-libdir/Repitools/libs/Repitools.so"
>>>>>>> Paths after fix:
Repitools.buildbin-libdir/Repitools/libs/Repitools.so:
Repitools.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)