| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -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 252/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrixMethods 1.70.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: BufferedMatrixMethods |
| Version: 1.70.0 |
| Command: rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BufferedMatrixMethods_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BufferedMatrixMethods.buildbin-libdir |
| StartedAt: 2024-12-20 12:01:41 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 12:01:50 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 8.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BufferedMatrixMethods_1.70.0.tgz |
| PackageFileSize: 53.13 KiB |
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### Running command:
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### rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BufferedMatrixMethods_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BufferedMatrixMethods.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BufferedMatrixMethods.buildbin-libdir BufferedMatrixMethods_1.70.0.tar.gz'
>>>>>>>
* installing *source* package ‘BufferedMatrixMethods’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-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/4.4-x86_64/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-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/4.4-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/4.4-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/4.4-x86_64/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)