##############################################################################
##############################################################################
###
### 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)
