Multiple platform build/check report for BioC 3.20 - CHECK results for Rhtslib on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for Rhtslib on palomino8

To the developers/maintainers of the Rhtslib package:
- 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 Troubleshooting Build Report for more information.
- 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: Rhtslib

Version: 3.2.0

Command: set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhtslib.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rhtslib_3.2.0.tar.gz

StartedAt: 2024-12-31 05:07:21 -0500 (Tue, 31 Dec 2024)

EndedAt: 2024-12-31 05:09:12 -0500 (Tue, 31 Dec 2024)

EllapsedTime: 111.1 seconds

RetCode: 0

Status: OK

CheckDir: Rhtslib.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhtslib.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rhtslib_3.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rhtslib/DESCRIPTION' ... OK
* this is package 'Rhtslib' version '3.2.0'
* package encoding: UTF-8
* 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:
  .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 whether package 'Rhtslib' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... NOTE
  installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs      10.3Mb
    testdata   4.7Mb
    usrlib     1.2Mb
* 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 code 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 whether startup messages can be suppressed ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/libs/x64/Rhtslib.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck/00check.log'
for details.

Installation output

Rhtslib.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rhtslib
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
cd "htslib-1.18" && /usr/bin/make -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/f/biocbuild/bbs-3.20-bioc/meat/Rhtslib/src/htslib-1.18'
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
if [ "x" != "x" ] && \
   [ "x" != "x" ] && \
   [ "x" != "x" ]; then \
    echo '#define HAVE_POPCNT 1' >> config.h ; \
    echo '#define HAVE_SSE4_1 1' >> config.h ; \
    echo '#define HAVE_SSSE3 1' >> config.h ; \
    echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \
    echo '#define UBSAN 1' >> config.h ; \
    echo '#endif' >> config.h ; \
fi
if [ "x" != "x" ] ; then \
    echo '#define HAVE_AVX2 1' >> config.h ; \
fi
if [ "x" != "x" ] ; then \
    echo '#define HAVE_AVX512 1' >> config.h ; \
fi
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.18"' > version.h
printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
'gcc' \
'-D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB' \
'-O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden' \
'-fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex' > config_vars.h
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam_mods.o sam_mods.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -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 sam_mods.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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o
ranlib libhts.a
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex/;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 '/f/biocbuild/bbs-3.20-bioc/meat/Rhtslib/src/htslib-1.18'
mkdir -p "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64"
cd "htslib-1.18" && cp libhts.a "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64"
mkdir -p "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.18/htslib" && cp * "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include/htslib"
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include" -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/testdata/tabix"
cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/libs/x64
** 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

name	user	system	elapsed
Rhtslib-package	0.01	0.00	0.02
pkgconfig	0.0	0.0	0.8