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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chopsticks_1.71.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.71.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chopsticks’ can be installed ... WARNING
Found the following significant warnings:
  adler32.c:57:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  adler32.c:128:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  compress.c:22:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  compress.c:62:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  compress.c:75:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:219:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:262:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:302:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:342:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:359:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:370:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:204:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:216:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:315:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:357:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:393:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:404:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:416:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:454:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:489:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:518:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:532:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:552:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:859:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:894:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:956:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:986:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1027:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1175:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1266:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1390:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1448:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  deflate.c:1554:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gzio.c:93:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:208:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:219:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:234:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:261:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:288:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:355:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:394:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:503:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:515:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:540:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:559:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:678:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:693:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:705:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:746:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:767:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:857:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:881:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:891:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:908:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:920:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:935:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:953:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:987:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  gzio.c:1017:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  infback.c:28:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  infback.c:73:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  infback.c:241:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  infback.c:614:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inffast.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:103:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:128:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:144:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:187:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:205:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:323:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:554:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1155:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1169:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1211:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1239:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1262:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1313:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inflate.c:1323:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inftrees.c:32:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  inputNew.c:612:17: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  trees.c:382:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:411:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:455:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:490:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:577:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:619:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:707:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:752:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:803:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:838:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:867:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:892:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:921:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1022:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1072:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1126:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1146:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1161:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1178:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  trees.c:1197:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  uncompr.c:26:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  zutil.c:133:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  zutil.c:300:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  zutil.c:310:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/chopsticks/libs/chopsticks.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
File ‘chopsticks/libs/chopsticks.so’:
  Found non-API call to R: ‘R_data_class’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chopsticks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘chopsticks’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c adler32.c -o adler32.o
adler32.c:57:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32(adler, buf, len)
              ^
adler32.c:128:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32_combine(adler1, adler2, len2)
              ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bind.c -o bind.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c compress.c -o compress.o
compress.c:22:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
            ^
compress.c:62:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT compress (dest, destLen, source, sourceLen)
            ^
compress.c:75:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT compressBound (sourceLen)
              ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c crc32.c -o crc32.o
crc32.c:219:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
unsigned long ZEXPORT crc32(crc, buf, len)
                      ^
crc32.c:262:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned long crc32_little(crc, buf, len)
                    ^
crc32.c:302:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned long crc32_big(crc, buf, len)
                    ^
crc32.c:342:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned long gf2_matrix_times(mat, vec)
                    ^
crc32.c:359:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void gf2_matrix_square(square, mat)
           ^
crc32.c:370:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine(crc1, crc2, len2)
              ^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c deflate.c -o deflate.o
deflate.c:204:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateInit_(strm, level, version, stream_size)
            ^
deflate.c:216:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
            ^
deflate.c:315:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
            ^
deflate.c:357:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateReset (strm)
            ^
deflate.c:393:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateSetHeader (strm, head)
            ^
deflate.c:404:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflatePrime (strm, bits, value)
            ^
deflate.c:416:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateParams(strm, level, strategy)
            ^
deflate.c:454:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
            ^
deflate.c:489:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT deflateBound(strm, sourceLen)
              ^
deflate.c:518:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void putShortMSB (s, b)
           ^
deflate.c:532:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void flush_pending(strm)
           ^
deflate.c:552:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflate (strm, flush)
            ^
deflate.c:859:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateEnd (strm)
            ^
deflate.c:894:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateCopy (dest, source)
            ^
deflate.c:956:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int read_buf(strm, buf, size)
          ^
deflate.c:986:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void lm_init (s)
           ^
deflate.c:1027:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local uInt longest_match(s, cur_match)
           ^
deflate.c:1175:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local uInt longest_match_fast(s, cur_match)
           ^
deflate.c:1266:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fill_window(s)
           ^
deflate.c:1390:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_stored(s, flush)
                  ^
deflate.c:1448:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_fast(s, flush)
                  ^
deflate.c:1554:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_slow(s, flush)
                  ^
22 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c force_hom.c -o force_hom.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c glm_test.c -o glm_test.o
glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
          (iter && (abs(wss-wss_last)/wss_last < conv));
                    ^
glm_test.c:155:14: note: use function 'fabs' instead
          (iter && (abs(wss-wss_last)/wss_last < conv));
                    ^~~
                    fabs
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c glm_test_R.c -o glm_test_R.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gzio.c -o gzio.o
gzio.c:93:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local gzFile gz_open (path, mode, fd)
             ^
gzio.c:208:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
gzFile ZEXPORT gzopen (path, mode)
               ^
gzio.c:219:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
gzFile ZEXPORT gzdopen (fd, mode)
               ^
gzio.c:234:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzsetparams (file, level, strategy)
            ^
gzio.c:261:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int get_byte(s)
          ^
gzio.c:288:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void check_header(s)
           ^
gzio.c:355:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int destroy (s)
          ^
gzio.c:394:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzread (file, buf, len)
            ^
gzio.c:503:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzgetc(file)
            ^
gzio.c:515:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzungetc(c, file)
            ^
gzio.c:540:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
char * ZEXPORT gzgets(file, buf, len)
               ^
gzio.c:559:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzwrite (file, buf, len)
            ^
gzio.c:678:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzputc(file, c)
            ^
gzio.c:693:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzputs(file, s)
            ^
gzio.c:705:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int do_flush (file, flush)
          ^
gzio.c:746:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzflush (file, flush)
            ^
gzio.c:767:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
z_off_t ZEXPORT gzseek (file, offset, whence)
                ^
gzio.c:857:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzrewind (file)
            ^
gzio.c:881:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
z_off_t ZEXPORT gztell (file)
                ^
gzio.c:891:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzeof (file)
            ^
gzio.c:908:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzdirect (file)
            ^
gzio.c:920:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void putLong (file, x)
           ^
gzio.c:935:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local uLong getLong (s)
            ^
gzio.c:953:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT gzclose (file)
            ^
gzio.c:987:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
const char * ZEXPORT gzerror (file, errnum)
                     ^
gzio.c:1017:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZEXPORT gzclearerr (file)
             ^
26 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hash_index.c -o hash_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ibs.c -o ibs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c in.c -o in.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c infback.c -o infback.o
infback.c:28:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
            ^
infback.c:73:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fixedtables(state)
           ^
infback.c:241:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
            ^
infback.c:614:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBackEnd(strm)
            ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inffast.c -o inffast.o
inffast.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void inflate_fast(strm, start)
     ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inflate.c -o inflate.o
inflate.c:103:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateReset(strm)
            ^
inflate.c:128:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflatePrime(strm, bits, value)
            ^
inflate.c:144:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
            ^
inflate.c:187:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateInit_(strm, version, stream_size)
            ^
inflate.c:205:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fixedtables(state)
           ^
inflate.c:323:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int updatewindow(strm, out)
          ^
inflate.c:554:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflate(strm, flush)
            ^
inflate.c:1155:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateEnd(strm)
            ^
inflate.c:1169:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
            ^
inflate.c:1211:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateGetHeader(strm, head)
            ^
inflate.c:1239:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned syncsearch(have, buf, len)
               ^
inflate.c:1262:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSync(strm)
            ^
inflate.c:1313:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSyncPoint(strm)
            ^
inflate.c:1323:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateCopy(dest, source)
            ^
14 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inftrees.c -o inftrees.o
inftrees.c:32:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int inflate_table(type, lens, codes, table, bits, work)
    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c input.c -o input.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inputNew.c -o inputNew.o
inputNew.c:612:17: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
      Rprintf("%d polymorphisms were not SNPs and have been set to NA ");
               ~^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c input_unsorted.c -o input_unsorted.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ld_graphic_eps.c -o ld_graphic_eps.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ld_with.c -o ld_with.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mla.c -o mla.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c outdata.c -o outdata.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pairwise_linkage.c -o pairwise_linkage.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_chiamo.c -o read_chiamo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_hapmap.c -o read_hapmap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_pedfile.c -o read_pedfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_signals.c -o read_signals.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readped.c -o readped.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sdfpw.c -o sdfpw.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c single_snp_tests.c -o single_snp_tests.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snp_summary.c -o snp_summary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snpmpy.c -o snpmpy.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c solve_cubic.c -o solve_cubic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c solve_quadratic.c -o solve_quadratic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c structure.c -o structure.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c trees.c -o trees.o
trees.c:382:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void _tr_init(s)
     ^
trees.c:411:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void init_block(s)
           ^
trees.c:455:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void pqdownheap(s, tree, k)
           ^
trees.c:490:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void gen_bitlen(s, desc)
           ^
trees.c:577:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void gen_codes (tree, max_code, bl_count)
           ^
trees.c:619:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void build_tree(s, desc)
           ^
trees.c:707:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void scan_tree (s, tree, max_code)
           ^
trees.c:752:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void send_tree (s, tree, max_code)
           ^
trees.c:803:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int build_bl_tree(s)
          ^
trees.c:838:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void send_all_trees(s, lcodes, dcodes, blcodes)
           ^
trees.c:867:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void _tr_stored_block(s, buf, stored_len, eof)
     ^
trees.c:892:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void _tr_align(s)
     ^
trees.c:921:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void _tr_flush_block(s, buf, stored_len, eof)
     ^
trees.c:1022:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int _tr_tally (s, dist, lc)
    ^
trees.c:1072:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void compress_block(s, ltree, dtree)
           ^
trees.c:1126:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void set_data_type(s)
           ^
trees.c:1146:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned bi_reverse(code, len)
               ^
trees.c:1161:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void bi_flush(s)
           ^
trees.c:1178:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void bi_windup(s)
           ^
trees.c:1197:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void copy_block(s, buf, len, header)
           ^
20 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c uncompr.c -o uncompr.o
uncompr.c:26:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT uncompress (dest, destLen, source, sourceLen)
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c zutil.c -o zutil.o
zutil.c:133:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
const char * ZEXPORT zError(err)
                     ^
zutil.c:300:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
voidpf zcalloc (opaque, items, size)
       ^
zutil.c:310:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void  zcfree (opaque, ptr)
      ^
3 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chopsticks.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-chopsticks/00new/chopsticks/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chopsticks)