##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Rhtslib_2.3.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Rhtslib.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* this is package ‘Rhtslib’ version ‘2.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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:
  .BBSoptions
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-3.18-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs       3.9Mb
    testdata   4.8Mb
    usrlib    12.8Mb
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Rhtslib.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘Rhtslib.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.161   0.040   0.195 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Rhtslib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
cd "htslib-1.15.1" && make -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/Rhtslib/src/htslib-1.15.1'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#ifndef _XOPEN_SOURCE' >> config.h
echo '#define _XOPEN_SOURCE 600' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I/usr/local/include -D_FILE_OFFSET_BITS=64"' >> config_vars.h
echo '#define HTS_CFLAGS "-g -O2 -fpic -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-L/usr/local/lib -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fpic -fvisibility=hidden -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 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o
ranlib libhts.a
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o header.pico header.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_expr.pico hts_expr.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o region.pico region.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fpic -fvisibility=hidden -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 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-soname,libhts.so.3 -L/usr/local/lib -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.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_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
ln -sf libhts.so libhts.so.3
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/Rhtslib/src/htslib-1.15.1'
mkdir -p "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include/htslib"
cd "htslib-1.15.1/htslib" && cp * "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include/htslib"
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include" -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib"
cd "htslib-1.15.1" && cp libhts.so libhts.a "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib"
cd "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.0/lib -lR
mkdir -p "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/testdata/tabix"
cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /home/biocbuild/R/R-4.3.0/site-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)