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CHECK report for Rhtslib on malbec1

This page was generated on 2020-04-15 12:09:46 -0400 (Wed, 15 Apr 2020).

Package 1432/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhtslib 1.18.1
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Rhtslib
Branch: RELEASE_3_10
Last Commit: 751a2eb
Last Changed Date: 2020-01-27 18:38:02 -0400 (Mon, 27 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rhtslib
Version: 1.18.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Rhtslib_1.18.1.tar.gz
StartedAt: 2020-04-15 02:50:01 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:50:16 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 15.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rhtslib.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Rhtslib_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Rhtslib.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhtslib’ version ‘1.18.1’
* 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:
  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 ‘/home/biocbuild/bbs-3.10-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs       2.2Mb
    testdata   4.2Mb
    usrlib     7.7Mb
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/htslib-1.7/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/libs/Rhtslib.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.



Installation output

Rhtslib.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Rhtslib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/home/biocbuild/bbs-3.10-bioc/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/biocbuild/bbs-3.10-bioc/meat/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/home/biocbuild/bbs-3.10-bioc/R/etc/Makeconf:168: warning: ignoring old recipe 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
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
gcc -g -O2  -Wall -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
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2  -Wall -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
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o knetfile.pico knetfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_net.pico hfile_net.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/files.pico cram/files.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-soname,libhts.so.2 -L/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
ln -sf libhts.so libhts.so.2
make[1]: Leaving directory '/home/biocbuild/bbs-3.10-bioc/meat/Rhtslib/src/htslib-1.7'
mkdir -p "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib"
cd "htslib-1.7" && cp libhts.so libhts.a "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib"
cd "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
mkdir -p "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /home/biocbuild/bbs-3.10-bioc/R/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)

Tests output


Example timings

Rhtslib.Rcheck/Rhtslib-Ex.timings

nameusersystemelapsed
Rhtslib-package0.0240.0000.024
pkgconfig0.0040.0000.002