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This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 258/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BufferedMatrixMethods 1.74.0  (landing page)
Ben Bolstad
Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025)
git_url: https://git.bioconductor.org/packages/BufferedMatrixMethods
git_branch: RELEASE_3_22
git_last_commit: e42f5a3
git_last_commit_date: 2025-10-29 09:58:58 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for BufferedMatrixMethods on lconway

To the developers/maintainers of the BufferedMatrixMethods package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrixMethods.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: BufferedMatrixMethods
Version: 1.74.0
Command: rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BufferedMatrixMethods_1.74.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BufferedMatrixMethods.buildbin-libdir
StartedAt: 2025-10-30 08:07:02 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 08:07:10 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 8.2 seconds
RetCode: 0
Status:   OK  
PackageFile: BufferedMatrixMethods_1.74.0.tgz
PackageFileSize: 53.79 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BufferedMatrixMethods_1.74.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BufferedMatrixMethods.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BufferedMatrixMethods.buildbin-libdir BufferedMatrixMethods_1.74.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BufferedMatrixMethods’ ...
** this is package ‘BufferedMatrixMethods’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BufferedMatrix/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BufferedMatrix/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable]
  int i,j;
      ^
preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
  int first_ind;
      ^
preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:453:12: warning: unused function 'min' [-Wunused-function]
static int min(int x1,int x2){
           ^
6 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 BufferedMatrixMethods.so init_package.o preprocess_bm.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrixMethods.buildbin-libdir/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (BufferedMatrixMethods)


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

>>>>>>> Paths before fix:
BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/BufferedMatrixMethods.so:
	BufferedMatrixMethods.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" "BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/BufferedMatrixMethods.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" "BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/BufferedMatrixMethods.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" "BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/BufferedMatrixMethods.so"

>>>>>>> Paths after fix:
BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/BufferedMatrixMethods.so:
	BufferedMatrixMethods.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)