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This page was generated on 2021-10-15 15:06:50 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Rhtslib package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhtslib.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. |
Package 1578/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhtslib 1.24.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Rhtslib |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhtslib_1.24.0.tar.gz |
StartedAt: 2021-10-14 23:11:06 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:11:30 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 24.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rhtslib.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhtslib_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rhtslib/DESCRIPTION’ ... OK * this is package ‘Rhtslib’ version ‘1.24.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt src/htslib-1.7/.appveyor.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rhtslib’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: testdata 4.2Mb usrlib 2.6Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/libs/Rhtslib.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_srand48’, possibly from ‘srand48’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck/00check.log’ for details.
Rhtslib.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib" Makefile.Rhtslib:128: warning: overriding commands for target `.c.o' /Library/Frameworks/R.framework/Resources/etc/Makeconf:168: warning: ignoring old commands for target `.c.o' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o ranlib libhts.a clang -mmacosx-version-min=10.13 -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.7 -compatibility_version 2 -L/usr/local/lib -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl ln -sf libhts.dylib libhts.2.dylib mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include" 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'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.a "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib" clang -mmacosx-version-min=10.13 -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 Rhtslib.so R_init_Rhtslib.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 mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/testdata/tabix" cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/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 * DONE (Rhtslib)
Rhtslib.Rcheck/Rhtslib-Ex.timings
name | user | system | elapsed | |
Rhtslib-package | 0.013 | 0.000 | 0.014 | |
pkgconfig | 0.001 | 0.001 | 0.003 | |