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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhtslib_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rhtslib.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* this is package ‘Rhtslib’ version ‘2.2.0’
* 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 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-3.17-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    testdata   4.8Mb
    usrlib     4.1Mb
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/libs/Rhtslib.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 ‘_sprintf’, possibly from ‘sprintf’ (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 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 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhtslib
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
cd "htslib-1.15.1" && make -f "Makefile.Rhtslib"
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
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/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 "clang -arch x86_64"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64"' >> config_vars.h
echo '#define HTS_CFLAGS "-falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-L/opt/R/x86_64/lib -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/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
clang -arch x86_64 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.15 -compatibility_version 3.1.15 -L/opt/R/x86_64/lib -fvisibility=hidden -o libhts.dylib 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 -lz -lm -lbz2 -llzma -lcurl
ln -sf libhts.dylib libhts.3.dylib
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
mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib"
cd "htslib-1.15.1/htslib" && cp * "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib"
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/usrlib"
cd "htslib-1.15.1" && cp libhts.a "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/usrlib"
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rhtslib.so R_init_Rhtslib.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-x86_64/Resources/library/Rhtslib/testdata/tabix"
cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-x86_64/Resources/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/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)