Lidia Chrabaszcz
| Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/GOpro |
| git_branch: RELEASE_3_16 |
| git_last_commit: 7f6cb6f |
| git_last_commit_date: 2022-11-01 11:14:32 -0400 (Tue, 01 Nov 2022) |
| Back to Mac ARM64 build report for BioC 3.16 |
|
This page was generated on 2023-04-19 11:01:55 -0400 (Wed, 19 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
| 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 | ||||
|
To the developers/maintainers of the GOpro package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 837/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
| GOpro 1.24.0 (landing page) Lidia Chrabaszcz
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | | |||||||
| Package: GOpro |
| Version: 1.24.0 |
| Command: rm -rf GOpro.buildbin-libdir && mkdir GOpro.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOpro_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GOpro.buildbin-libdir |
| StartedAt: 2023-04-18 16:13:16 -0400 (Tue, 18 Apr 2023) |
| EndedAt: 2023-04-18 16:14:45 -0400 (Tue, 18 Apr 2023) |
| EllapsedTime: 88.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: GOpro_1.24.0.tgz |
| PackageFileSize: 1.349 MiB |
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###
### Running command:
###
### rm -rf GOpro.buildbin-libdir && mkdir GOpro.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOpro_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GOpro.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GOpro.buildbin-libdir GOpro_1.24.0.tar.gz'
>>>>>>>
* installing *source* package ‘GOpro’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GOpro_init.c -o GOpro_init.o
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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fisher.cpp -o fisher.o
In file included from fisher.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/hypergeometric.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/detail/common_error_handling.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/policies/error_handling.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/throw_exception.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: 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]
std::sprintf( buffer, ":%ld", static_cast<long>( line() ) );
^
/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)))
^
In file included from fisher.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/hypergeometric.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/detail/common_error_handling.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/policies/error_handling.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/throw_exception.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: 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]
std::sprintf( buffer, ":%ld", static_cast<long>( column() ) );
^
/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)))
^
In file included from fisher.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/hypergeometric.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/detail/hypergeometric_pdf.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/constants/constants.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/lexical_cast.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: 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(begin,
^
/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)))
^
In file included from fisher.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/hypergeometric.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/detail/hypergeometric_pdf.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/constants/constants.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/lexical_cast.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: 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(begin,
^
/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)))
^
In file included from fisher.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/hypergeometric.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/distributions/detail/hypergeometric_pdf.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/constants/constants.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/math/tools/lexical_cast.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: 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(begin,
^
/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)))
^
5 warnings 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 GOpro.so GOpro_init.o RcppExports.o fisher.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/GOpro.buildbin-libdir/00LOCK-GOpro/00new/GOpro/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (GOpro)
>>>>>>>
>>>>>>> FIXING LINKS FOR GOpro.buildbin-libdir/GOpro/libs/GOpro.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" "GOpro.buildbin-libdir/GOpro/libs/GOpro.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" "GOpro.buildbin-libdir/GOpro/libs/GOpro.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" "GOpro.buildbin-libdir/GOpro/libs/GOpro.so"