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This page was generated on 2023-04-19 11:01:54 -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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INSTALL results for contiBAIT on kjohnson


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

raw results

Package 408/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
contiBAIT 1.26.0  (landing page)
Kieran O'Neill
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/contiBAIT
git_branch: RELEASE_3_16
git_last_commit: e8a94bc
git_last_commit_date: 2022-11-01 11:12:55 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: contiBAIT
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL contiBAIT
StartedAt: 2023-04-16 17:00:22 -0400 (Sun, 16 Apr 2023)
EndedAt: 2023-04-16 17:02:16 -0400 (Sun, 16 Apr 2023)
EllapsedTime: 114.0 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL contiBAIT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* installing *source* package ‘contiBAIT’ ...
** 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'/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 buildLinkageGroups.cpp -o buildLinkageGroups.o
In file included from buildLinkageGroups.cpp:1:
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 computeSim.cpp -o computeSim.o
In file included from computeSim.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)))
                                                      ^
In file included from computeSim.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:52:
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 computeSim.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:52:
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)))
                                                      ^
3 warnings 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 orderContigsGreedy.cpp -o orderContigsGreedy.o
In file included from orderContigsGreedy.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 contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-contiBAIT/00new/contiBAIT/libs
** R
** data
** 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 (contiBAIT)