| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-03 12:03 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 15/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ADAM 1.26.0 (landing page) Jose Luiz Rybarczyk Filho
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the ADAM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADAM.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: ADAM |
| Version: 1.26.0 |
| Command: rm -rf ADAM.buildbin-libdir && mkdir ADAM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ADAM_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ADAM.buildbin-libdir |
| StartedAt: 2025-11-03 01:27:26 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 01:28:18 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 52.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: ADAM_1.26.0.tgz |
| PackageFileSize: 398.2 KiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ADAM.buildbin-libdir && mkdir ADAM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ADAM_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ADAM.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ADAM.buildbin-libdir ADAM_1.26.0.tar.gz'
>>>>>>>
* installing *source* package ‘ADAM’ ...
** this is package ‘ADAM’ version ‘1.26.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MakeBootstrap.cpp -o MakeBootstrap.o
MakeBootstrap.cpp:9:9: warning: variable 'k' set but not used [-Wunused-but-set-variable]
int k = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ADAM.so MakeBootstrap.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/ADAM.buildbin-libdir/00LOCK-ADAM/00new/ADAM/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 (ADAM)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ADAM.buildbin-libdir/ADAM/libs/ADAM.so
>>>>>>>
>>>>>>> Paths before fix:
ADAM.buildbin-libdir/ADAM/libs/ADAM.so:
ADAM.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/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" "ADAM.buildbin-libdir/ADAM/libs/ADAM.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" "ADAM.buildbin-libdir/ADAM/libs/ADAM.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" "ADAM.buildbin-libdir/ADAM/libs/ADAM.so"
>>>>>>> Paths after fix:
ADAM.buildbin-libdir/ADAM/libs/ADAM.so:
ADAM.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)