##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhtslib.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rhtslib_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Rhtslib.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rhtslib/DESCRIPTION' ... OK
* this is package 'Rhtslib' version '1.28.0'
* 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:
  .BBSoptions
  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 whether package 'Rhtslib' can be installed ... WARNING
Found the following significant warnings:
  bgzf.c:566:23: warning: too many arguments for format [-Wformat-extra-args]
  bgzf.c:888:31: warning: too many arguments for format [-Wformat-extra-args]
  faidx.c:76:25: warning: too many arguments for format [-Wformat-extra-args]
  faidx.c:222:27: warning: too many arguments for format [-Wformat-extra-args]
  multipart.c:81:27: warning: too many arguments for format [-Wformat-extra-args]
  sam.c:1439:29: warning: too many arguments for format [-Wformat-extra-args]
  sam.c:233:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  cram/cram_io.c:2071:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
  cram/cram_io.c:2178:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
  cram/cram_io.c:3677:6: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
  cram/cram_io.c:3669:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
  cram/cram_io.c:4055:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation]
  cram/string_alloc.c:151:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
Found the following additional notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.15-bioc/meat/Rhtslib.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs       6.6Mb
    testdata   4.1Mb
    usrlib     4.7Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-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)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (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
  'F:/biocbuild/bbs-3.15-bioc/meat/Rhtslib.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rhtslib
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && /usr/bin/make -f "F:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:128: warning: overriding recipe for target '.c.o'
F:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf:253: warning: ignoring old recipe for target '.c.o'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o kfunc.o kfunc.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o knetfile.o knetfile.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o kstring.o kstring.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o bgzf.o bgzf.c
In file included from htslib/hts.h:35,
                 from bgzf.c:38:
bgzf.c: In function 'load_block_from_cache':
bgzf.c:566:23: warning: unknown conversion type character 'l' in format [-Wformat=]
  566 |         hts_log_error("Could not hseek to %"PRId64"", p->end_offset);
      |                       ^~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
bgzf.c:566:23: warning: too many arguments for format [-Wformat-extra-args]
  566 |         hts_log_error("Could not hseek to %"PRId64"", p->end_offset);
      |                       ^~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
bgzf.c: In function 'bgzf_read':
bgzf.c:888:31: warning: unknown conversion type character 'z' in format [-Wformat=]
  888 |                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
bgzf.c:888:81: note: format string is defined here
  888 |                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
      |                                                                                 ^
In file included from htslib/hts.h:35,
                 from bgzf.c:38:
bgzf.c:888:31: warning: unknown conversion type character 'z' in format [-Wformat=]
  888 |                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
bgzf.c:888:88: note: format string is defined here
  888 |                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
      |                                                                                        ^
In file included from htslib/hts.h:35,
                 from bgzf.c:38:
bgzf.c:888:31: warning: too many arguments for format [-Wformat-extra-args]
  888 |                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o errmod.o errmod.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o faidx.o faidx.c
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from faidx.c:43:
faidx.c: In function 'fai_insert_index':
faidx.c:76:25: warning: unknown conversion type character 'l' in format [-Wformat=]
   76 |         hts_log_warning("Ignoring duplicate sequence \"%s\" at byte offset %"PRIu64"", name, offset);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
   78 | #define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
      |                                                                 ^~~~~~~~~~~
faidx.c:76:25: warning: too many arguments for format [-Wformat-extra-args]
   76 |         hts_log_warning("Ignoring duplicate sequence \"%s\" at byte offset %"PRIu64"", name, offset);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
   78 | #define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
      |                                                                 ^~~~~~~~~~~
faidx.c: In function 'fai_read':
faidx.c:222:27: warning: unknown conversion type character 'z' in format [-Wformat=]
  222 |             hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
faidx.c:222:62: note: format string is defined here
  222 |             hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
      |                                                              ^
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from faidx.c:43:
faidx.c:222:27: warning: too many arguments for format [-Wformat-extra-args]
  222 |             hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
   75 | #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o hfile.o hfile.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o hts.o hts.c
hts.c: In function 'hts_idx_init':
hts.c:1366:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow]
 1366 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
      |                                                           ^~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o hts_os.o hts_os.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o md5.o md5.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o multipart.o multipart.c
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from multipart.c:33:
multipart.c: In function 'multipart_read':
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
   84 | #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
multipart.c:81:43: note: format string is defined here
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                                           ^
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from multipart.c:33:
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
   84 | #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
multipart.c:81:50: note: format string is defined here
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                                                  ^
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from multipart.c:33:
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   82 |                 fp->current+1, fp->nparts, p->url,
      |                 ~~~~~~~~~~~~~
      |                            |
      |                            size_t {aka long long unsigned int}
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
   84 | #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
multipart.c:81:61: note: format string is defined here
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                                                        ~~~~~^
      |                                                             |
      |                                                             char *
      |                                                        %.120I64d
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from multipart.c:33:
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   82 |                 fp->current+1, fp->nparts, p->url,
      |                                ~~~~~~~~~~
      |                                  |
      |                                  size_t {aka long long unsigned int}
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
   84 | #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
multipart.c:81:63: note: format string is defined here
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                                                              ~^
      |                                                               |
      |                                                               char *
      |                                                              %I64d
In file included from htslib/hts.h:35,
                 from hts_internal.h:29,
                 from multipart.c:33:
multipart.c:81:27: warning: too many arguments for format [-Wformat-extra-args]
   81 |             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
   84 | #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
      |                                                             ^~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o probaln.o probaln.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o realn.o realn.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o regidx.o regidx.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o sam.o sam.c
In file included from htslib/hts.h:35,
                 from htslib/sam.h:31,
                 from sam.c:35:
sam.c: In function 'sam_read1':
sam.c:1439:29: warning: unknown conversion type character 'l' in format [-Wformat=]
 1439 |             hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
   78 | #define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
      |                                                                 ^~~~~~~~~~~
sam.c:1439:52: note: format string is defined here
 1439 |             hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
      |                                                    ^
In file included from htslib/hts.h:35,
                 from htslib/sam.h:31,
                 from sam.c:35:
sam.c:1439:29: warning: too many arguments for format [-Wformat-extra-args]
 1439 |             hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
   78 | #define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
      |                                                                 ^~~~~~~~~~~
sam.c: In function 'bam_hdr_write':
sam.c:233:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  233 |     strncpy(buf, "BAM\1", 4);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o tbx.o tbx.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o textutils.o textutils.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o vcf.o vcf.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
In file included from ./textutils_internal.h:32,
                 from ./hts_internal.h:31,
                 from cram/cram_index.c:65:
In function 'kputsn',
    inlined from 'kputs' at ./htslib/kstring.h:156:9,
    inlined from 'cram_index_build' at cram/cram_index.c:571:9:
./htslib/kstring.h:148:2: warning: 'memcpy' specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  148 |  memcpy(s->s + s->l, p, l);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:2071:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
 2071 |  strncpy(path, path2, PATH_MAX);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2178:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |                           ^~~~~
cram/cram_io.c:2178:6: note: 'sprintf' output between 11 and 298 bytes into a destination of size 260
 2178 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
    inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3752:3:
cram/cram_io.c:3677:6: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
 3677 |      strncpy(out, in, PATH_MAX);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:3669:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
 3669 |  strncpy(out, in, PATH_MAX);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c: In function 'cram_dopen':
cram/cram_io.c:4055:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation]
 4055 |  strncpy(def->file_id, filename, 20);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/files.o cram/files.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/rANS_static.o cram/rANS_static.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/sam_header.o cram/sam_header.c
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
In function 'string_ndup',
    inlined from 'string_dup' at cram/string_alloc.c:143:12:
cram/string_alloc.c:151:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  151 |     strncpy(str, instr, len);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
cram/string_alloc.c: In function 'string_dup':
cram/string_alloc.c:143:12: note: length computed here
  143 |     return string_ndup(a_str, instr, strlen(instr));
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/rtools42/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -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  -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import  -o cyghts-2.dll -Wl,--whole-archive 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 -Wl,--no-whole-archive -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -lpthread
make[1]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/Rhtslib/src/htslib-1.7'
mkdir -p "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64"
cd "htslib-1.7" && cp libhts.a "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64"
mkdir -p "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include"
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.15-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-3.15-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-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-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)