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This page was generated on 2023-04-19 11:01:56 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for mosaics on kjohnson


To the developers/maintainers of the mosaics package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1250/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
mosaics 2.36.0  (landing page)
Dongjun Chung
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/mosaics
git_branch: RELEASE_3_16
git_last_commit: 3166c3a
git_last_commit_date: 2022-11-01 11:05:34 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mosaics
Version: 2.36.0
Command: rm -rf mosaics.buildbin-libdir && mkdir mosaics.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mosaics_2.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mosaics.buildbin-libdir
StartedAt: 2023-04-18 17:29:54 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 17:31:53 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 119.2 seconds
RetCode: 0
Status:   OK  
PackageFile: mosaics_2.36.0.tgz
PackageFileSize: 1.816 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf mosaics.buildbin-libdir && mkdir mosaics.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mosaics_2.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mosaics.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mosaics.buildbin-libdir mosaics_2.36.0.tar.gz'
>>>>>>> 

* installing *source* package ‘mosaics’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c convolution_1S.cpp -o convolution_1S.o
In file included from convolution_1S.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c convolution_2S.cpp -o convolution_2S.o
In file included from convolution_2S.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c emHMM.cpp -o emHMM.o
In file included from emHMM.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c stack.cpp -o stack.o
In file included from stack.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c updatePiMat.cpp -o updatePiMat.o
In file included from updatePiMat.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c viterbi.cpp -o viterbi.o
In file included from viterbi.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -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 mosaics.so convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/mosaics.buildbin-libdir/00LOCK-mosaics/00new/mosaics/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 (mosaics)


>>>>>>> 
>>>>>>> FIXING LINKS FOR mosaics.buildbin-libdir/mosaics/libs/mosaics.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "mosaics.buildbin-libdir/mosaics/libs/mosaics.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "mosaics.buildbin-libdir/mosaics/libs/mosaics.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "mosaics.buildbin-libdir/mosaics/libs/mosaics.so"