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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 149/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bcSeq 1.28.0  (landing page)
Jiaxing Lin
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/bcSeq
git_branch: RELEASE_3_20
git_last_commit: bb5c125
git_last_commit_date: 2024-10-29 10:24:12 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for bcSeq on kjohnson3

To the developers/maintainers of the bcSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bcSeq.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: bcSeq
Version: 1.28.0
Command: rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.28.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bcSeq.buildbin-libdir
StartedAt: 2024-11-09 16:38:36 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 16:38:49 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 12.2 seconds
RetCode: 0
Status:   OK  
PackageFile: bcSeq_1.28.0.tgz
PackageFileSize: 350.6 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.28.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bcSeq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bcSeq.buildbin-libdir bcSeq_1.28.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bcSeq’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from CRISPR_matching.cpp:3:
In file included from ./helper/count.h:6:
./helper/fastqCheck.h:54:26: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      sequence.push_back(move(line));
                         ^
                         std::
./helper/fastqCheck.h:55:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      sequence_ids.push_back(move(id));
                             ^
                             std::
./helper/fastqCheck.h:56:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      phredScore.push_back(move(phred));
                           ^
                           std::
In file included from CRISPR_matching.cpp:3:
./helper/count.h:37:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      library.push_back(move(line));
                        ^
                        std::
./helper/count.h:38:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      library_ids.push_back(move(id));
                            ^
                            std::
./helper/count.h:72:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      library.push_back(move(line));
                        ^
                        std::
./helper/count.h:73:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
      library_ids.push_back(move(id));
                            ^
                            std::
7 warnings 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Trie_edit.cpp -o Trie_edit.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Trie_hamming.cpp -o Trie_hamming.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Trie_util.cpp -o Trie_util.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c alignment.cpp -o alignment.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c trimRead.cpp -o trimRead.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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include   -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c uniqueBar.cpp -o uniqueBar.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 bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/bcSeq.buildbin-libdir/00LOCK-bcSeq/00new/bcSeq/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 (bcSeq)


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

>>>>>>> Paths before fix:
bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so:
	bcSeq.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 4.4.1)
	/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"

>>>>>>> Paths after fix:
bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so:
	bcSeq.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 4.4.1)
	/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)