Aaron Lun
| Snapshot Date: 2023-10-15 14:00:07 -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) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1858/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| screenCounter 1.0.1 (landing page) Aaron Lun
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the screenCounter package: - 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: 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: 2023-10-19 17:02:37 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 17:05:47 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 189.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: screenCounter_1.0.1.tgz |
| PackageFileSize: 477.5 KiB |
##############################################################################
##############################################################################
###
### 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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch arm64 -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/arm64/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-mac-arm64/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-arm64/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-arm64/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-arm64/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-arm64/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-arm64/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)