Benilton S Carvalho
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/crlmm |
| git_branch: RELEASE_3_20 |
| git_last_commit: f1bd3c9 |
| git_last_commit_date: 2024-10-29 09:31:05 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 464/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crlmm 1.64.0 (landing page) Benilton S Carvalho
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the crlmm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crlmm.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: crlmm |
| Version: 1.64.0 |
| Command: rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.64.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R crlmm.buildbin-libdir |
| StartedAt: 2024-12-21 14:28:34 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 14:29:21 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 46.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: crlmm_1.64.0.tgz |
| PackageFileSize: 5.201 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.64.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R crlmm.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=crlmm.buildbin-libdir crlmm_1.64.0.tar.gz'
>>>>>>>
* installing *source* package ‘crlmm’ ...
** 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/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gtypeCaller.c -o gtypeCaller.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trimmed.c -o trimmed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
utils.c:81:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
utils.c:81:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
utils.c:81:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
utils.c:207:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
utils.c:207:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
utils.c:207:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
6 warnings generated.
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 crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** testing if installed package keeps a record of temporary installation path
* DONE (crlmm)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR crlmm.buildbin-libdir/crlmm/libs/crlmm.so
>>>>>>>
>>>>>>> Paths before fix:
crlmm.buildbin-libdir/crlmm/libs/crlmm.so:
crlmm.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 4.4.2)
/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" "crlmm.buildbin-libdir/crlmm/libs/crlmm.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "crlmm.buildbin-libdir/crlmm/libs/crlmm.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "crlmm.buildbin-libdir/crlmm/libs/crlmm.so"
>>>>>>> Paths after fix:
crlmm.buildbin-libdir/crlmm/libs/crlmm.so:
crlmm.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 4.4.2)
/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)