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###
### Running command:
###
###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings Rhtslib_2.3.0.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/Rhtslib.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
    GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* 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 ... 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 ... WARNING
Found the following significant warnings:
  hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
Found the following additional notes/warnings:
  Non-staged installation was used
See ‘/home/hpages/bbs-3.18-bioc-testing/meat/Rhtslib.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
* checking installed package size ... NOTE
  installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs       2.9Mb
    testdata   4.8Mb
    usrlib    10.4Mb
* 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 loading without being on the library search path ... 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 ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/libs/Rhtslib.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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 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 ...
  ‘Rhtslib.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/hpages/bbs-3.18-bioc-testing/meat/Rhtslib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL Rhtslib
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
cd "htslib-1.15.1" && make -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/hpages/bbs-3.18-bioc-testing/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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
gcc -g -O2 -Wall -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 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -g -O2 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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
In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74:
In function ‘RansEncFlush’,
    inlined from ‘rans_compress_O1_4x16.isra’ at htscodecs/htscodecs/rANS_static4x16pr.c:840:5:
htscodecs/htscodecs/rANS_word.h:109:9: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  109 |     ptr -= 4;
      |     ~~~~^~~~
htscodecs/htscodecs/rANS_static4x16pr.c: In function ‘rans_compress_O1_4x16.isra’:
htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: ‘ptr’ was declared here
  793 |     uint8_t* ptr = out_end;
      |              ^~~
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
hfile_libcurl.c: In function ‘libcurl_open’:
hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
 1335 |         if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
      |         ^~
In file included from hfile_libcurl.c:47:
/usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here
 2858 |   CURLINFO_CONTENT_LENGTH_DOWNLOAD
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
gcc -g -O2 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o header.pico header.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_expr.pico hts_expr.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o region.pico region.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
gcc -g -O2 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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
In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74:
In function ‘RansEncFlush’,
    inlined from ‘rans_compress_O1_4x16.isra’ at htscodecs/htscodecs/rANS_static4x16pr.c:840:5:
htscodecs/htscodecs/rANS_word.h:109:9: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  109 |     ptr -= 4;
      |     ~~~~^~~~
htscodecs/htscodecs/rANS_static4x16pr.c: In function ‘rans_compress_O1_4x16.isra’:
htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: ‘ptr’ was declared here
  793 |     uint8_t* ptr = out_end;
      |              ^~~
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
hfile_libcurl.c: In function ‘libcurl_open’:
hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
 1335 |         if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
      |         ^~
In file included from hfile_libcurl.c:47:
/usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here
 2858 |   CURLINFO_CONTENT_LENGTH_DOWNLOAD
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/hpages/bbs-3.18-bioc-testing/meat/Rhtslib/src/htslib-1.15.1'
mkdir -p "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include/htslib"
cd "htslib-1.15.1/htslib" && cp * "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include/htslib"
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include" -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/usrlib"
cd "htslib-1.15.1" && cp libhts.so libhts.a "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/usrlib"
cd "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/usrlib/libhts.a -lcurl
mkdir -p "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/testdata/tabix"
cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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)