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This page was generated on 2023-04-19 11:01:53 -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 BitSeq on kjohnson


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

raw results

Package 208/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
BitSeq 1.42.0  (landing page)
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/BitSeq
git_branch: RELEASE_3_16
git_last_commit: 17d08b9
git_last_commit_date: 2022-11-01 11:06:51 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  ERROR    ERROR  skipped

Summary

Package: BitSeq
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BitSeq
StartedAt: 2023-04-16 16:10:03 -0400 (Sun, 16 Apr 2023)
EndedAt: 2023-04-16 16:10:36 -0400 (Sun, 16 Apr 2023)
EllapsedTime: 32.2 seconds
RetCode: 1
Status:   ERROR  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.42.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++14 accepts -g... yes
checking for clang++ -arch arm64 -std=gnu++14 option to support OpenMP... unsupported
configure: No Open MP support.
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c ArgumentParser.cpp -o ArgumentParser.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c CollapsedSampler.cpp -o CollapsedSampler.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c FileHeader.cpp -o FileHeader.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c GibbsParameters.cpp -o GibbsParameters.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c GibbsSampler.cpp -o GibbsSampler.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c MyTimer.cpp -o MyTimer.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c PosteriorSamples.cpp -o PosteriorSamples.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include  -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c ReadDistribution.cpp -o ReadDistribution.o
In file included from ReadDistribution.cpp:7:
./ReadDistribution.h:13:10: fatal error: 'bam.h' file not found
#include "bam.h"
         ^~~~~~~
1 error generated.
make: *** [ReadDistribution.o] Error 1
ERROR: compilation failed for package ‘BitSeq’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BitSeq’