##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chopsticks.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings chopsticks_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chopsticks/DESCRIPTION' ... OK
* this is package 'chopsticks' version '1.73.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'chopsticks' can be installed ... WARNING
Found the following significant warnings:
  glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:408:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:406:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:404:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:401:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:398:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:395:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  readped.c:233:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=]
See 'E:/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether 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 ... NOTE
checkRd: (-1) for.exercise.Rd:29-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) for.exercise.Rd:34-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) for.exercise.Rd:40-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glm.test.control.Rd:30-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) glm.test.control.Rd:33-37: Lost braces in \enumerate; meant \describe ?
prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references
prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso
prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note
checkRd: (-1) read.snps.long.old.Rd:81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) read.snps.long.old.Rd:82: Lost braces in \enumerate; meant \describe ?
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
checkRd: (-1) read.wtccc.signals.Rd:30: Escaped LaTeX specials: \_ \_
checkRd: (-1) snp.lhs.tests.Rd:36: Lost braces
    36 |     new terms to be tested. See\ code{\link{glm.test.control}}}
       |                                      ^
checkRd: (-1) snp.rhs.tests.Rd:42: Lost braces
    42 |     new terms to be tested. See\ code{\link{glm.test.control}}}
       |                                      ^
checkRd: (-1) snpMatrix-package.Rd:21: Escaped LaTeX specials: \_ \_
checkRd: (-1) testdata.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:33-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:39: Lost braces in \itemize; meant \describe ?
prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note
prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples
checkRd: (-1) wtccc.sample.list.Rd:26: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'snpMatrix-package.Rd':
  'snpMatrix-package'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL chopsticks
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'chopsticks' ...
** this is package 'chopsticks' version '1.73.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c adler32.c -o adler32.o
adler32.c: In function 'adler32':
adler32.c:57:15: warning: old-style function definition [-Wold-style-definition]
   57 | uLong ZEXPORT adler32(adler, buf, len)
      |               ^~~~~~~
adler32.c: In function 'adler32_combine':
adler32.c:128:15: warning: old-style function definition [-Wold-style-definition]
  128 | uLong ZEXPORT adler32_combine(adler1, adler2, len2)
      |               ^~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c bind.c -o bind.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c compress.c -o compress.o
compress.c: In function 'compress2':
compress.c:22:13: warning: old-style function definition [-Wold-style-definition]
   22 | int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
      |             ^~~~~~~~~
compress.c: In function 'compress':
compress.c:62:13: warning: old-style function definition [-Wold-style-definition]
   62 | int ZEXPORT compress (dest, destLen, source, sourceLen)
      |             ^~~~~~~~
compress.c: In function 'compressBound':
compress.c:75:15: warning: old-style function definition [-Wold-style-definition]
   75 | uLong ZEXPORT compressBound (sourceLen)
      |               ^~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c crc32.c -o crc32.o
crc32.c: In function 'crc32':
crc32.c:219:23: warning: old-style function definition [-Wold-style-definition]
  219 | unsigned long ZEXPORT crc32(crc, buf, len)
      |                       ^~~~~
crc32.c: In function 'crc32_little':
crc32.c:262:21: warning: old-style function definition [-Wold-style-definition]
  262 | local unsigned long crc32_little(crc, buf, len)
      |                     ^~~~~~~~~~~~
crc32.c: In function 'crc32_big':
crc32.c:302:21: warning: old-style function definition [-Wold-style-definition]
  302 | local unsigned long crc32_big(crc, buf, len)
      |                     ^~~~~~~~~
crc32.c: In function 'gf2_matrix_times':
crc32.c:342:21: warning: old-style function definition [-Wold-style-definition]
  342 | local unsigned long gf2_matrix_times(mat, vec)
      |                     ^~~~~~~~~~~~~~~~
crc32.c: In function 'gf2_matrix_square':
crc32.c:359:12: warning: old-style function definition [-Wold-style-definition]
  359 | local void gf2_matrix_square(square, mat)
      |            ^~~~~~~~~~~~~~~~~
crc32.c: In function 'crc32_combine':
crc32.c:370:15: warning: old-style function definition [-Wold-style-definition]
  370 | uLong ZEXPORT crc32_combine(crc1, crc2, len2)
      |               ^~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c deflate.c -o deflate.o
deflate.c: In function 'deflateInit_':
deflate.c:204:13: warning: old-style function definition [-Wold-style-definition]
  204 | int ZEXPORT deflateInit_(strm, level, version, stream_size)
      |             ^~~~~~~~~~~~
deflate.c: In function 'deflateInit2_':
deflate.c:216:13: warning: old-style function definition [-Wold-style-definition]
  216 | int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
      |             ^~~~~~~~~~~~~
deflate.c: In function 'deflateSetDictionary':
deflate.c:315:13: warning: old-style function definition [-Wold-style-definition]
  315 | int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
      |             ^~~~~~~~~~~~~~~~~~~~
deflate.c: In function 'deflateReset':
deflate.c:357:13: warning: old-style function definition [-Wold-style-definition]
  357 | int ZEXPORT deflateReset (strm)
      |             ^~~~~~~~~~~~
deflate.c: In function 'deflateSetHeader':
deflate.c:393:13: warning: old-style function definition [-Wold-style-definition]
  393 | int ZEXPORT deflateSetHeader (strm, head)
      |             ^~~~~~~~~~~~~~~~
deflate.c: In function 'deflatePrime':
deflate.c:404:13: warning: old-style function definition [-Wold-style-definition]
  404 | int ZEXPORT deflatePrime (strm, bits, value)
      |             ^~~~~~~~~~~~
deflate.c: In function 'deflateParams':
deflate.c:416:13: warning: old-style function definition [-Wold-style-definition]
  416 | int ZEXPORT deflateParams(strm, level, strategy)
      |             ^~~~~~~~~~~~~
deflate.c: In function 'deflateTune':
deflate.c:454:13: warning: old-style function definition [-Wold-style-definition]
  454 | int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
      |             ^~~~~~~~~~~
deflate.c: In function 'deflateBound':
deflate.c:489:15: warning: old-style function definition [-Wold-style-definition]
  489 | uLong ZEXPORT deflateBound(strm, sourceLen)
      |               ^~~~~~~~~~~~
deflate.c: In function 'putShortMSB':
deflate.c:518:12: warning: old-style function definition [-Wold-style-definition]
  518 | local void putShortMSB (s, b)
      |            ^~~~~~~~~~~
deflate.c: In function 'flush_pending':
deflate.c:532:12: warning: old-style function definition [-Wold-style-definition]
  532 | local void flush_pending(strm)
      |            ^~~~~~~~~~~~~
deflate.c: In function 'deflate':
deflate.c:552:13: warning: old-style function definition [-Wold-style-definition]
  552 | int ZEXPORT deflate (strm, flush)
      |             ^~~~~~~
deflate.c: In function 'deflateEnd':
deflate.c:859:13: warning: old-style function definition [-Wold-style-definition]
  859 | int ZEXPORT deflateEnd (strm)
      |             ^~~~~~~~~~
deflate.c: In function 'deflateCopy':
deflate.c:894:13: warning: old-style function definition [-Wold-style-definition]
  894 | int ZEXPORT deflateCopy (dest, source)
      |             ^~~~~~~~~~~
deflate.c: In function 'read_buf':
deflate.c:956:11: warning: old-style function definition [-Wold-style-definition]
  956 | local int read_buf(strm, buf, size)
      |           ^~~~~~~~
deflate.c: In function 'lm_init':
deflate.c:986:12: warning: old-style function definition [-Wold-style-definition]
  986 | local void lm_init (s)
      |            ^~~~~~~
deflate.c: In function 'longest_match':
deflate.c:1027:12: warning: old-style function definition [-Wold-style-definition]
 1027 | local uInt longest_match(s, cur_match)
      |            ^~~~~~~~~~~~~
deflate.c: In function 'longest_match_fast':
deflate.c:1175:12: warning: old-style function definition [-Wold-style-definition]
 1175 | local uInt longest_match_fast(s, cur_match)
      |            ^~~~~~~~~~~~~~~~~~
deflate.c: In function 'fill_window':
deflate.c:1266:12: warning: old-style function definition [-Wold-style-definition]
 1266 | local void fill_window(s)
      |            ^~~~~~~~~~~
deflate.c: In function 'deflate_stored':
deflate.c:1390:19: warning: old-style function definition [-Wold-style-definition]
 1390 | local block_state deflate_stored(s, flush)
      |                   ^~~~~~~~~~~~~~
deflate.c: In function 'deflate_fast':
deflate.c:1448:19: warning: old-style function definition [-Wold-style-definition]
 1448 | local block_state deflate_fast(s, flush)
      |                   ^~~~~~~~~~~~
deflate.c: In function 'deflate_slow':
deflate.c:1554:19: warning: old-style function definition [-Wold-style-definition]
 1554 | local block_state deflate_slow(s, flush)
      |                   ^~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c force_hom.c -o force_hom.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  107 |       double *yw = (double *) calloc(N, sizeof(double));
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from glm_test.c:1:
C:/rtools45/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here
  536 |   void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
      |                 ^~~~~~
glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  107 |       double *yw = (double *) calloc(N, sizeof(double));
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here
  536 |   void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
      |                 ^~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c glm_test_R.c -o glm_test_R.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c gzio.c -o gzio.o
gzio.c: In function 'gz_open':
gzio.c:93:14: warning: old-style function definition [-Wold-style-definition]
   93 | local gzFile gz_open (path, mode, fd)
      |              ^~~~~~~
gzio.c: In function 'gzopen':
gzio.c:208:16: warning: old-style function definition [-Wold-style-definition]
  208 | gzFile ZEXPORT gzopen (path, mode)
      |                ^~~~~~
gzio.c: In function 'gzdopen':
gzio.c:219:16: warning: old-style function definition [-Wold-style-definition]
  219 | gzFile ZEXPORT gzdopen (fd, mode)
      |                ^~~~~~~
gzio.c: In function 'gzsetparams':
gzio.c:234:13: warning: old-style function definition [-Wold-style-definition]
  234 | int ZEXPORT gzsetparams (file, level, strategy)
      |             ^~~~~~~~~~~
gzio.c: In function 'get_byte':
gzio.c:261:11: warning: old-style function definition [-Wold-style-definition]
  261 | local int get_byte(s)
      |           ^~~~~~~~
gzio.c: In function 'check_header':
gzio.c:288:12: warning: old-style function definition [-Wold-style-definition]
  288 | local void check_header(s)
      |            ^~~~~~~~~~~~
gzio.c: In function 'destroy':
gzio.c:355:11: warning: old-style function definition [-Wold-style-definition]
  355 | local int destroy (s)
      |           ^~~~~~~
gzio.c: In function 'gzread':
gzio.c:394:13: warning: old-style function definition [-Wold-style-definition]
  394 | int ZEXPORT gzread (file, buf, len)
      |             ^~~~~~
gzio.c: In function 'gzgetc':
gzio.c:503:13: warning: old-style function definition [-Wold-style-definition]
  503 | int ZEXPORT gzgetc(file)
      |             ^~~~~~
gzio.c: In function 'gzungetc':
gzio.c:515:13: warning: old-style function definition [-Wold-style-definition]
  515 | int ZEXPORT gzungetc(c, file)
      |             ^~~~~~~~
gzio.c: In function 'gzgets':
gzio.c:540:16: warning: old-style function definition [-Wold-style-definition]
  540 | char * ZEXPORT gzgets(file, buf, len)
      |                ^~~~~~
gzio.c: In function 'gzwrite':
gzio.c:559:13: warning: old-style function definition [-Wold-style-definition]
  559 | int ZEXPORT gzwrite (file, buf, len)
      |             ^~~~~~~
gzio.c: In function 'gzputc':
gzio.c:678:13: warning: old-style function definition [-Wold-style-definition]
  678 | int ZEXPORT gzputc(file, c)
      |             ^~~~~~
gzio.c: In function 'gzputs':
gzio.c:693:13: warning: old-style function definition [-Wold-style-definition]
  693 | int ZEXPORT gzputs(file, s)
      |             ^~~~~~
gzio.c: In function 'do_flush':
gzio.c:705:11: warning: old-style function definition [-Wold-style-definition]
  705 | local int do_flush (file, flush)
      |           ^~~~~~~~
gzio.c: In function 'gzflush':
gzio.c:746:13: warning: old-style function definition [-Wold-style-definition]
  746 | int ZEXPORT gzflush (file, flush)
      |             ^~~~~~~
gzio.c: In function 'gzseek':
gzio.c:767:17: warning: old-style function definition [-Wold-style-definition]
  767 | z_off_t ZEXPORT gzseek (file, offset, whence)
      |                 ^~~~~~
gzio.c: In function 'gzrewind':
gzio.c:857:13: warning: old-style function definition [-Wold-style-definition]
  857 | int ZEXPORT gzrewind (file)
      |             ^~~~~~~~
gzio.c: In function 'gztell':
gzio.c:881:17: warning: old-style function definition [-Wold-style-definition]
  881 | z_off_t ZEXPORT gztell (file)
      |                 ^~~~~~
gzio.c: In function 'gzeof':
gzio.c:891:13: warning: old-style function definition [-Wold-style-definition]
  891 | int ZEXPORT gzeof (file)
      |             ^~~~~
gzio.c: In function 'gzdirect':
gzio.c:908:13: warning: old-style function definition [-Wold-style-definition]
  908 | int ZEXPORT gzdirect (file)
      |             ^~~~~~~~
gzio.c: In function 'putLong':
gzio.c:920:12: warning: old-style function definition [-Wold-style-definition]
  920 | local void putLong (file, x)
      |            ^~~~~~~
gzio.c: In function 'getLong':
gzio.c:935:13: warning: old-style function definition [-Wold-style-definition]
  935 | local uLong getLong (s)
      |             ^~~~~~~
gzio.c: In function 'gzclose':
gzio.c:953:13: warning: old-style function definition [-Wold-style-definition]
  953 | int ZEXPORT gzclose (file)
      |             ^~~~~~~
gzio.c: In function 'gzerror':
gzio.c:987:22: warning: old-style function definition [-Wold-style-definition]
  987 | const char * ZEXPORT gzerror (file, errnum)
      |                      ^~~~~~~
gzio.c: In function 'gzclearerr':
gzio.c:1017:14: warning: old-style function definition [-Wold-style-definition]
 1017 | void ZEXPORT gzclearerr (file)
      |              ^~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c hash_index.c -o hash_index.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ibs.c -o ibs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c in.c -o in.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c infback.c -o infback.o
infback.c: In function 'inflateBackInit_':
infback.c:28:13: warning: old-style function definition [-Wold-style-definition]
   28 | int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
      |             ^~~~~~~~~~~~~~~~
infback.c: In function 'fixedtables':
infback.c:73:12: warning: old-style function definition [-Wold-style-definition]
   73 | local void fixedtables(state)
      |            ^~~~~~~~~~~
infback.c: In function 'inflateBack':
infback.c:241:13: warning: old-style function definition [-Wold-style-definition]
  241 | int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
      |             ^~~~~~~~~~~
infback.c: In function 'inflateBackEnd':
infback.c:614:13: warning: old-style function definition [-Wold-style-definition]
  614 | int ZEXPORT inflateBackEnd(strm)
      |             ^~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c inffast.c -o inffast.o
inffast.c: In function 'inflate_fast':
inffast.c:67:6: warning: old-style function definition [-Wold-style-definition]
   67 | void inflate_fast(strm, start)
      |      ^~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c inflate.c -o inflate.o
inflate.c: In function 'inflateReset':
inflate.c:103:13: warning: old-style function definition [-Wold-style-definition]
  103 | int ZEXPORT inflateReset(strm)
      |             ^~~~~~~~~~~~
inflate.c: In function 'inflatePrime':
inflate.c:128:13: warning: old-style function definition [-Wold-style-definition]
  128 | int ZEXPORT inflatePrime(strm, bits, value)
      |             ^~~~~~~~~~~~
inflate.c: In function 'inflateInit2_':
inflate.c:144:13: warning: old-style function definition [-Wold-style-definition]
  144 | int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
      |             ^~~~~~~~~~~~~
inflate.c: In function 'inflateInit_':
inflate.c:187:13: warning: old-style function definition [-Wold-style-definition]
  187 | int ZEXPORT inflateInit_(strm, version, stream_size)
      |             ^~~~~~~~~~~~
inflate.c: In function 'fixedtables':
inflate.c:205:12: warning: old-style function definition [-Wold-style-definition]
  205 | local void fixedtables(state)
      |            ^~~~~~~~~~~
inflate.c: In function 'updatewindow':
inflate.c:323:11: warning: old-style function definition [-Wold-style-definition]
  323 | local int updatewindow(strm, out)
      |           ^~~~~~~~~~~~
inflate.c: In function 'inflate':
inflate.c:554:13: warning: old-style function definition [-Wold-style-definition]
  554 | int ZEXPORT inflate(strm, flush)
      |             ^~~~~~~
inflate.c: In function 'inflateEnd':
inflate.c:1155:13: warning: old-style function definition [-Wold-style-definition]
 1155 | int ZEXPORT inflateEnd(strm)
      |             ^~~~~~~~~~
inflate.c: In function 'inflateSetDictionary':
inflate.c:1169:13: warning: old-style function definition [-Wold-style-definition]
 1169 | int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
      |             ^~~~~~~~~~~~~~~~~~~~
inflate.c: In function 'inflateGetHeader':
inflate.c:1211:13: warning: old-style function definition [-Wold-style-definition]
 1211 | int ZEXPORT inflateGetHeader(strm, head)
      |             ^~~~~~~~~~~~~~~~
inflate.c: In function 'syncsearch':
inflate.c:1239:16: warning: old-style function definition [-Wold-style-definition]
 1239 | local unsigned syncsearch(have, buf, len)
      |                ^~~~~~~~~~
inflate.c: In function 'inflateSync':
inflate.c:1262:13: warning: old-style function definition [-Wold-style-definition]
 1262 | int ZEXPORT inflateSync(strm)
      |             ^~~~~~~~~~~
inflate.c: In function 'inflateSyncPoint':
inflate.c:1313:13: warning: old-style function definition [-Wold-style-definition]
 1313 | int ZEXPORT inflateSyncPoint(strm)
      |             ^~~~~~~~~~~~~~~~
inflate.c: In function 'inflateCopy':
inflate.c:1323:13: warning: old-style function definition [-Wold-style-definition]
 1323 | int ZEXPORT inflateCopy(dest, source)
      |             ^~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c inftrees.c -o inftrees.o
inftrees.c: In function 'inflate_table':
inftrees.c:32:5: warning: old-style function definition [-Wold-style-definition]
   32 | int inflate_table(type, lens, codes, table, bits, work)
      |     ^~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c input.c -o input.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c inputNew.c -o inputNew.o
inputNew.c: In function 'simplify_names':
inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  687 |     strncpy(back, front, MAX_FLD-1);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c: In function 'insnp_new':
inputNew.c:408:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  408 |           strncpy(gtype2, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:406:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  406 |           strncpy(gtype1, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:404:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  404 |           strncpy(gtype1, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:401:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  401 |           strncpy(cscore, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:398:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  398 |           strncpy(snpid, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:395:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  395 |           strncpy(sampid, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c input_unsorted.c -o input_unsorted.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ld_with.c -o ld_with.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c mla.c -o mla.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c outdata.c -o outdata.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c pairwise_linkage.c -o pairwise_linkage.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c read_chiamo.c -o read_chiamo.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c read_hapmap.c -o read_hapmap.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c read_pedfile.c -o read_pedfile.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c read_signals.c -o read_signals.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c readped.c -o readped.o
readped.c: In function 'readped':
readped.c:233:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=]
  233 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |                                 ^~
readped.c:233:5: note: 'snprintf' output between 3 and 93 bytes into a destination of size 81
  233 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c sdfpw.c -o sdfpw.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c single_snp_tests.c -o single_snp_tests.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c snp_summary.c -o snp_summary.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c snpmpy.c -o snpmpy.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c solve_cubic.c -o solve_cubic.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c solve_quadratic.c -o solve_quadratic.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c structure.c -o structure.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c trees.c -o trees.o
trees.c: In function '_tr_init':
trees.c:382:6: warning: old-style function definition [-Wold-style-definition]
  382 | void _tr_init(s)
      |      ^~~~~~~~
trees.c: In function 'init_block':
trees.c:411:12: warning: old-style function definition [-Wold-style-definition]
  411 | local void init_block(s)
      |            ^~~~~~~~~~
trees.c: In function 'pqdownheap':
trees.c:455:12: warning: old-style function definition [-Wold-style-definition]
  455 | local void pqdownheap(s, tree, k)
      |            ^~~~~~~~~~
trees.c: In function 'gen_bitlen':
trees.c:490:12: warning: old-style function definition [-Wold-style-definition]
  490 | local void gen_bitlen(s, desc)
      |            ^~~~~~~~~~
trees.c: In function 'gen_codes':
trees.c:577:12: warning: old-style function definition [-Wold-style-definition]
  577 | local void gen_codes (tree, max_code, bl_count)
      |            ^~~~~~~~~
trees.c: In function 'build_tree':
trees.c:619:12: warning: old-style function definition [-Wold-style-definition]
  619 | local void build_tree(s, desc)
      |            ^~~~~~~~~~
trees.c: In function 'scan_tree':
trees.c:707:12: warning: old-style function definition [-Wold-style-definition]
  707 | local void scan_tree (s, tree, max_code)
      |            ^~~~~~~~~
trees.c: In function 'send_tree':
trees.c:752:12: warning: old-style function definition [-Wold-style-definition]
  752 | local void send_tree (s, tree, max_code)
      |            ^~~~~~~~~
trees.c: In function 'build_bl_tree':
trees.c:803:11: warning: old-style function definition [-Wold-style-definition]
  803 | local int build_bl_tree(s)
      |           ^~~~~~~~~~~~~
trees.c: In function 'send_all_trees':
trees.c:838:12: warning: old-style function definition [-Wold-style-definition]
  838 | local void send_all_trees(s, lcodes, dcodes, blcodes)
      |            ^~~~~~~~~~~~~~
trees.c: In function '_tr_stored_block':
trees.c:867:6: warning: old-style function definition [-Wold-style-definition]
  867 | void _tr_stored_block(s, buf, stored_len, eof)
      |      ^~~~~~~~~~~~~~~~
trees.c: In function '_tr_align':
trees.c:892:6: warning: old-style function definition [-Wold-style-definition]
  892 | void _tr_align(s)
      |      ^~~~~~~~~
trees.c: In function '_tr_flush_block':
trees.c:921:6: warning: old-style function definition [-Wold-style-definition]
  921 | void _tr_flush_block(s, buf, stored_len, eof)
      |      ^~~~~~~~~~~~~~~
trees.c: In function '_tr_tally':
trees.c:1022:5: warning: old-style function definition [-Wold-style-definition]
 1022 | int _tr_tally (s, dist, lc)
      |     ^~~~~~~~~
trees.c: In function 'compress_block':
trees.c:1072:12: warning: old-style function definition [-Wold-style-definition]
 1072 | local void compress_block(s, ltree, dtree)
      |            ^~~~~~~~~~~~~~
trees.c: In function 'set_data_type':
trees.c:1126:12: warning: old-style function definition [-Wold-style-definition]
 1126 | local void set_data_type(s)
      |            ^~~~~~~~~~~~~
trees.c: In function 'bi_reverse':
trees.c:1146:16: warning: old-style function definition [-Wold-style-definition]
 1146 | local unsigned bi_reverse(code, len)
      |                ^~~~~~~~~~
trees.c: In function 'bi_flush':
trees.c:1161:12: warning: old-style function definition [-Wold-style-definition]
 1161 | local void bi_flush(s)
      |            ^~~~~~~~
trees.c: In function 'bi_windup':
trees.c:1178:12: warning: old-style function definition [-Wold-style-definition]
 1178 | local void bi_windup(s)
      |            ^~~~~~~~~
trees.c: In function 'copy_block':
trees.c:1197:12: warning: old-style function definition [-Wold-style-definition]
 1197 | local void copy_block(s, buf, len, header)
      |            ^~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c uncompr.c -o uncompr.o
uncompr.c: In function 'uncompress':
uncompr.c:26:13: warning: old-style function definition [-Wold-style-definition]
   26 | int ZEXPORT uncompress (dest, destLen, source, sourceLen)
      |             ^~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c zutil.c -o zutil.o
zutil.c: In function 'zError':
zutil.c:133:22: warning: old-style function definition [-Wold-style-definition]
  133 | const char * ZEXPORT zError(err)
      |                      ^~~~~~
zutil.c: In function 'zcalloc':
zutil.c:300:8: warning: old-style function definition [-Wold-style-definition]
  300 | voidpf zcalloc (opaque, items, size)
      |        ^~~~~~~
zutil.c: In function 'zcfree':
zutil.c:310:7: warning: old-style function definition [-Wold-style-definition]
  310 | void  zcfree (opaque, ptr)
      |       ^~~~~~
gcc -shared -s -static-libgcc -o chopsticks.dll tmp.def adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-chopsticks/00new/chopsticks/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chopsticks)