##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rhtslib_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* this is package ‘Rhtslib’ version ‘1.24.0’
* 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 ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  cram/cram_io.c:2178:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
Found the following additional notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs       1.4Mb
    testdata   1.7Mb
    usrlib     5.0Mb
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/libs/Rhtslib.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (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. 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rhtslib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/home/biocbuild/bbs-3.13-bioc/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/home/biocbuild/bbs-3.13-bioc/R/etc/Makeconf:168: 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
echo '#define HAVE_LIBCURL 1' >> config.h
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
In file included from /usr/include/string.h:495,
                 from sam.c:31:
In function ‘strncpy’,
    inlined from ‘bam_hdr_write’ at sam.c:233:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2  -Wall -fpic -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 -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 -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 -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
In file included from /usr/include/string.h:495,
                 from cram/cram_index.c:57:
In function ‘memcpy’,
    inlined from ‘kputsn’ at ./htslib/kstring.h:148:2,
    inlined from ‘kputs’ at ./htslib/kstring.h:156:9,
    inlined from ‘cram_index_build’ at cram/cram_index.c:571:9:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   34 |   return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function ‘cram_populate_ref’:
cram/cram_io.c:2178:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |                           ^~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |                        ^~~~~~~~~~~~~~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:867,
                 from cram/cram_io.c:49:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from cram/cram_io.c:53:
In function ‘strncpy’,
    inlined from ‘cram_populate_ref’ at cram/cram_io.c:2071:2:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3677:6,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3752:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3669:2,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3752:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2  -Wall -fpic -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 -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.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 hfile_libcurl.o
ranlib libhts.a
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o knetfile.pico knetfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_net.pico hfile_net.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
In file included from /usr/include/string.h:495,
                 from sam.c:31:
In function ‘strncpy’,
    inlined from ‘bam_hdr_write’ at sam.c:233:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
gcc -g -O2  -Wall -fpic -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 -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 -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 -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_index.pico cram/cram_index.c
In file included from /usr/include/string.h:495,
                 from cram/cram_index.c:57:
In function ‘memcpy’,
    inlined from ‘kputsn’ at ./htslib/kstring.h:148:2,
    inlined from ‘kputs’ at ./htslib/kstring.h:156:9,
    inlined from ‘cram_index_build’ at cram/cram_index.c:571:9:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   34 |   return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_io.pico cram/cram_io.c
cram/cram_io.c: In function ‘cram_populate_ref’:
cram/cram_io.c:2178:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |                           ^~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |                        ^~~~~~~~~~~~~~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:867,
                 from cram/cram_io.c:49:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from cram/cram_io.c:53:
In function ‘strncpy’,
    inlined from ‘cram_populate_ref’ at cram/cram_io.c:2071:2:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3677:6,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3752:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3669:2,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3752:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/files.pico cram/files.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2  -Wall -fpic -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 -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2  -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2  -Wall -fpic -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 -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-soname,libhts.so.2 -L/usr/local/lib -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 hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
ln -sf libhts.so libhts.so.2
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/Rhtslib/src/htslib-1.7'
mkdir -p "/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include"
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include" -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rhtslib/usrlib"
cd "htslib-1.7" && cp libhts.so libhts.a "/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib"
cd "/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
mkdir -p "/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /home/biocbuild/bbs-3.13-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)