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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 962/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HEM 1.80.0  (landing page)
HyungJun Cho
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/HEM
git_branch: RELEASE_3_21
git_last_commit: 0c872b2
git_last_commit_date: 2025-04-15 09:34:45 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for HEM on merida1

To the developers/maintainers of the HEM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HEM.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: HEM
Version: 1.80.0
Command: rm -rf HEM.buildbin-libdir && mkdir HEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HEM_1.80.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HEM.buildbin-libdir
StartedAt: 2025-10-14 13:41:49 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 13:42:13 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 23.7 seconds
RetCode: 0
Status:   OK  
PackageFile: HEM_1.80.0.tgz
PackageFileSize: 717.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HEM.buildbin-libdir && mkdir HEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HEM_1.80.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HEM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HEM.buildbin-libdir HEM_1.80.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HEM’ ...
** this is package ‘HEM’ version ‘1.80.0’
** 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/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hem.c -o hem.o
hem.c:1390:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
        int i, j, k, m, n;
                  ^
hem.c:1593:16: warning: variable 'l' set but not used [-Wunused-but-set-variable]
  int i, j, k, l;
               ^
2 warnings generated.
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 HEM.so hem.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/HEM.buildbin-libdir/00LOCK-HEM/00new/HEM/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 (HEM)


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

>>>>>>> Paths before fix:
HEM.buildbin-libdir/HEM/libs/HEM.so:
	HEM.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "HEM.buildbin-libdir/HEM/libs/HEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "HEM.buildbin-libdir/HEM/libs/HEM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "HEM.buildbin-libdir/HEM/libs/HEM.so"

>>>>>>> Paths after fix:
HEM.buildbin-libdir/HEM/libs/HEM.so:
	HEM.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)