Multiple platform build/check report for BioC 3.9 - CHECK report for Rhtslib on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rhtslib_1.15.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.5’
* 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-3.9-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    testdata   4.2Mb
    usrlib     7.5Mb
* 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
* 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-3.9-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rhtslib
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/home/biocbuild/bbs-3.9-bioc/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/home/biocbuild/bbs-3.9-bioc/R/etc/Makeconf:166: 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
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.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
ranlib libhts.a
gcc -g -Wall -O2 -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -I.  -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -I.  -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -I.  -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -I.  -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -I.  -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -I.  -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -I.  -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -I.  -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -I.  -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -I.  -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2  -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 -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
make[1]: Leaving directory '/home/biocbuild/bbs-3.9-bioc/meat/Rhtslib/src/htslib-1.7'
mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/Rhtslib/usrlib"
cd "htslib-1.7" && cp libhts.so libhts.a "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib"
cd "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o -L/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
mkdir -p "/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
Rhtslib-package	0.015	0.000	0.015
pkgconfig	0.001	0.000	0.002

CHECK report for Rhtslib on malbec2

Summary

Command output

Installation output

Tests output

Example timings