Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1885/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.48.0  (landing page)
Daniel Jones
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/seqbias
git_branch: RELEASE_3_17
git_last_commit: 7e94228
git_last_commit_date: 2023-04-25 10:18:39 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  ERROR    ERROR  skippedskipped

INSTALL results for seqbias on kjohnson2


To the developers/maintainers of the seqbias package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: seqbias
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqbias
StartedAt: 2023-10-15 15:38:37 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 15:38:46 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 8.6 seconds
RetCode: 1
Status:   ERROR  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
$SEQBIAS_OBJ is [common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o]
$YAML_CPP_OBJ is [aliasmanager.o conversion.o directives.o emitfromevents.o emitter.o emitterstate.o emitterutils.o exp.o iterator.o nodebuilder.o node.o nodeownership.o null.o ostream.o parser.o regex.o scanner.o scanscalar.o scantag.o scantoken.o simplekey.o singledocparser.o stream.o tag.o]
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include   -Wall -Wextra -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c common.c -o common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include   -Wall -Wextra -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c miscmath.c -o miscmath.o
miscmath.c:21:12: error: implicitly declaring library function 'finite' with type 'int (double)' [-Werror,-Wimplicit-function-declaration]
    return finite(a) && 0.0 <= a && a <= 1.0;
           ^
miscmath.c:21:12: note: include the header <math.h> or explicitly provide a declaration for 'finite'
1 error generated.
make: *** [miscmath.o] Error 1
ERROR: compilation failed for package ‘seqbias’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqbias’