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This page was generated on 2024-12-12 12:09 -0500 (Thu, 12 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4462
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 2056/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
srnadiff 1.26.0  (landing page)
Zytnicki Matthias
Snapshot Date: 2024-12-09 13:00 -0500 (Mon, 09 Dec 2024)
git_url: https://git.bioconductor.org/packages/srnadiff
git_branch: RELEASE_3_20
git_last_commit: 705e506
git_last_commit_date: 2024-10-29 10:25:16 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    TIMEOUT    OK  

BUILD BIN results for srnadiff on kjohnson1

To the developers/maintainers of the srnadiff package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/srnadiff.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: srnadiff
Version: 1.26.0
Command: rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh srnadiff_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R srnadiff.buildbin-libdir
StartedAt: 2024-12-11 16:43:29 -0500 (Wed, 11 Dec 2024)
EndedAt: 2024-12-11 16:44:57 -0500 (Wed, 11 Dec 2024)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:   OK  
PackageFile: srnadiff_1.26.0.tgz
PackageFileSize: 2.894 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh srnadiff_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R srnadiff.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=srnadiff.buildbin-libdir srnadiff_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘srnadiff’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
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/4.4-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/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_hmm.cpp -o rcpp_hmm.o
rcpp_hmm.cpp:109:17: warning: variable 'cpt' set but not used [-Wunused-but-set-variable]
            int cpt = 0;
                ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_ir.cpp -o rcpp_ir.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_main.cpp -o rcpp_main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_utils.cpp -o rcpp_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c srnadiff_init.c -o srnadiff_init.o
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 srnadiff.so RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/srnadiff.buildbin-libdir/00LOCK-srnadiff/00new/srnadiff/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** testing if installed package keeps a record of temporary installation path
* DONE (srnadiff)


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

>>>>>>> Paths before fix:
srnadiff.buildbin-libdir/srnadiff/libs/srnadiff.so:
	srnadiff.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/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/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "srnadiff.buildbin-libdir/srnadiff/libs/srnadiff.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "srnadiff.buildbin-libdir/srnadiff/libs/srnadiff.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "srnadiff.buildbin-libdir/srnadiff/libs/srnadiff.so"

>>>>>>> Paths after fix:
srnadiff.buildbin-libdir/srnadiff/libs/srnadiff.so:
	srnadiff.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/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/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)