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This page was generated on 2023-10-16 11:37:31 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1858/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
screenCounter 1.0.1  (landing page)
Aaron Lun
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/screenCounter
git_branch: RELEASE_3_17
git_last_commit: 3f8596c
git_last_commit_date: 2023-07-02 19:07:07 -0400 (Sun, 02 Jul 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD BIN results for screenCounter on merida1


To the developers/maintainers of the screenCounter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/screenCounter.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: screenCounter
Version: 1.0.1
Command: rm -rf screenCounter.buildbin-libdir && mkdir screenCounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh screenCounter_1.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R screenCounter.buildbin-libdir
StartedAt: 2023-10-16 10:11:07 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 10:15:22 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 255.2 seconds
RetCode: 0
Status:   OK  
PackageFile: screenCounter_1.0.1.tgz
PackageFileSize: 483.3 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf screenCounter.buildbin-libdir && mkdir screenCounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh screenCounter_1.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R screenCounter.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=screenCounter.buildbin-libdir screenCounter_1.0.1.tar.gz'
>>>>>>> 

* installing *source* package ‘screenCounter’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_combo_barcodes_paired.cpp -o count_combo_barcodes_paired.o
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_combo_barcodes_single.cpp -o count_combo_barcodes_single.o
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
In file included from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_dual_barcodes.cpp -o count_dual_barcodes.o
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_random_barcodes.cpp -o count_random_barcodes.o
In file included from count_random_barcodes.cpp:3:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable 'found' [-Wunused-variable]
        bool found = false;
             ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_single_barcodes.cpp -o count_single_barcodes.o
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o screenCounter.so RcppExports.o count_combo_barcodes_paired.o count_combo_barcodes_single.o count_dual_barcodes.o count_random_barcodes.o count_single_barcodes.o utils.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/screenCounter.buildbin-libdir/00LOCK-screenCounter/00new/screenCounter/libs
** R
** 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 (screenCounter)


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

>>>>>>> Paths before fix:
screenCounter.buildbin-libdir/screenCounter/libs/screenCounter.so:
	screenCounter.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "screenCounter.buildbin-libdir/screenCounter/libs/screenCounter.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "screenCounter.buildbin-libdir/screenCounter/libs/screenCounter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "screenCounter.buildbin-libdir/screenCounter/libs/screenCounter.so"

>>>>>>> Paths after fix:
screenCounter.buildbin-libdir/screenCounter/libs/screenCounter.so:
	screenCounter.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)