Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-03 11:45 -0500 (Tue, 03 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4461
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4405
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4360
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 1457
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 698/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEAST 1.15.0  (landing page)
Kenong Su
Snapshot Date: 2024-12-02 13:40 -0500 (Mon, 02 Dec 2024)
git_url: https://git.bioconductor.org/packages/FEAST
git_branch: devel
git_last_commit: 169e892
git_last_commit_date: 2024-10-29 10:59:00 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD BIN results for FEAST on kjohnson3

To the developers/maintainers of the FEAST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FEAST.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: FEAST
Version: 1.15.0
Command: rm -rf FEAST.buildbin-libdir && mkdir FEAST.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FEAST_1.15.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FEAST.buildbin-libdir
StartedAt: 2024-12-03 07:01:04 -0500 (Tue, 03 Dec 2024)
EndedAt: 2024-12-03 07:01:18 -0500 (Tue, 03 Dec 2024)
EllapsedTime: 14.3 seconds
RetCode: 0
Status:   OK  
PackageFile: FEAST_1.15.0.tgz
PackageFileSize: 4.567 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf FEAST.buildbin-libdir && mkdir FEAST.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FEAST_1.15.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FEAST.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=FEAST.buildbin-libdir FEAST_1.15.0.tar.gz'
>>>>>>> 

* installing *source* package ‘FEAST’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cal_3_metrics.c -o cal_3_metrics.o
cal_3_metrics.c:42:22: warning: variable 'ni_2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                     ^
cal_3_metrics.c:42:28: warning: variable 'n_j2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                           ^
cal_3_metrics.c:42:34: warning: variable 'nt' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                                 ^
cal_3_metrics.c:42:38: warning: variable 'nij_2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                                     ^
4 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 FEAST.so cal_3_metrics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/FEAST.buildbin-libdir/00LOCK-FEAST/00new/FEAST/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (FEAST)


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

>>>>>>> Paths before fix:
FEAST.buildbin-libdir/FEAST/libs/FEAST.so:
	FEAST.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "FEAST.buildbin-libdir/FEAST/libs/FEAST.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "FEAST.buildbin-libdir/FEAST/libs/FEAST.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "FEAST.buildbin-libdir/FEAST/libs/FEAST.so"

>>>>>>> Paths after fix:
FEAST.buildbin-libdir/FEAST/libs/FEAST.so:
	FEAST.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)