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This page was generated on 2021-10-15 15:06:52 -0400 (Fri, 15 Oct 2021).

INSTALL results for seqbias on machv2

To the developers/maintainers of the seqbias package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqbias.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1732/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.40.0  (landing page)
Daniel Jones
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/seqbias
git_branch: RELEASE_3_13
git_last_commit: c9d8e78
git_last_commit_date: 2021-05-19 11:47:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    ERROR  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: seqbias
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqbias
StartedAt: 2021-10-14 08:29:45 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 08:31:06 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c sam.c -o sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c bam_aux.c -o bam_aux.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c common.c -o common.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c miscmath.c -o miscmath.o
miscmath.c:21:12: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
    return finite(a) && 0.0 <= a && a <= 1.0;
           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/math.h:749:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double)
           ^
miscmath.c:47:9: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
    if (finite(u)) return x + log1p(-exp(u));
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/math.h:749:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double)
           ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c pos_table.c -o pos_table.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c kmer_matrix.cpp -o kmer_matrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c logger.cpp -o logger.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c motif.cpp -o motif.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c seqbias.cpp -o seqbias.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c sequencing_bias.cpp -o sequencing_bias.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c twobitseq.cpp -o twobitseq.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/node.cpp -o yaml-cpp/node.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/null.cpp -o yaml-cpp/null.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
                void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
                                                             ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include  -Wall -Wextra -I. -fPIC  -Wall -g -O2  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o seqbias.so sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-seqbias/00new/seqbias/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 (seqbias)