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This page was generated on 2025-10-16 11:40 -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 2097/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRACIPE 2.0.1  (landing page)
Mingyang Lu
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/sRACIPE
git_branch: RELEASE_3_21
git_last_commit: 1c51770
git_last_commit_date: 2025-05-08 12:30:27 -0400 (Thu, 08 May 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  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for sRACIPE on kjohnson1

To the developers/maintainers of the sRACIPE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sRACIPE.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: sRACIPE
Version: 2.0.1
Command: rm -rf sRACIPE.buildbin-libdir && mkdir sRACIPE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sRACIPE_2.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sRACIPE.buildbin-libdir
StartedAt: 2025-10-15 20:42:44 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 20:43:49 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 65.0 seconds
RetCode: 0
Status:   OK  
PackageFile: sRACIPE_2.0.1.tgz
PackageFileSize: 1.006 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sRACIPE.buildbin-libdir && mkdir sRACIPE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sRACIPE_2.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sRACIPE.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sRACIPE.buildbin-libdir sRACIPE_2.0.1.tar.gz'
>>>>>>> 

* installing *source* package ‘sRACIPE’ ...
** this is package ‘sRACIPE’ version ‘2.0.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c generateThresholds.cpp -o generateThresholds.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c header.cpp -o header.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c limitcycle.cpp -o limitcycle.o
limitcycle.cpp:327:9: warning: variable 'countSameMinDist' set but not used [-Wunused-but-set-variable]
    int countSameMinDist=0;
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c simulateGRC.cpp -o simulateGRC.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c steppers.cpp -o steppers.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c steppersConv.cpp -o steppersConv.o
steppersConv.cpp:37:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  double i=0.0;
         ^
steppersConv.cpp:170:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
double i=0.0;
       ^
steppersConv.cpp:422:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  double i=0.0;
         ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o limitcycle.o simulateGRC.o steppers.o steppersConv.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/sRACIPE.buildbin-libdir/00LOCK-sRACIPE/00new/sRACIPE/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 (sRACIPE)


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

>>>>>>> Paths before fix:
sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so:
	sRACIPE.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 4.5.1)
	/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so"

>>>>>>> Paths after fix:
sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so:
	sRACIPE.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 4.5.1)
	/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)