Hin-Tak Leung
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/chopsticks |
| git_branch: RELEASE_3_20 |
| git_last_commit: ba6aa9b |
| git_last_commit_date: 2024-10-29 09:35:52 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 344/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chopsticks 1.72.0 (landing page) Hin-Tak Leung
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the chopsticks package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chopsticks.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: chopsticks |
| Version: 1.72.0 |
| 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_1.72.0.tar.gz |
| StartedAt: 2024-12-20 14:28:59 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 14:30:10 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 70.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chopsticks.Rcheck |
| Warnings: 3 |
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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_1.72.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.72.0’
* 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 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-1500.0.40.1)’
* 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.
chopsticks.Rcheck/00install.out
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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-1500.0.40.1)’
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)
chopsticks.Rcheck/chopsticks-Ex.timings
| name | user | system | elapsed | |
| X.snp-class | 0.133 | 0.015 | 0.149 | |
| X.snp.matrix-class | 0.119 | 0.008 | 0.127 | |
| epsout.ld.snp | 0.181 | 0.014 | 0.195 | |
| for.exercise | 0.838 | 0.034 | 0.874 | |
| ibs.stats | 0.119 | 0.008 | 0.127 | |
| ibsCount | 0.250 | 0.007 | 0.258 | |
| ibsDist | 0.158 | 0.006 | 0.164 | |
| ld.snp | 0.172 | 0.006 | 0.178 | |
| ld.with | 0.122 | 0.006 | 0.129 | |
| pair.result.ld.snp | 0.112 | 0.005 | 0.117 | |
| plot.snp.dprime | 0.295 | 0.016 | 0.315 | |
| qq.chisq | 0 | 0 | 0 | |
| read.HapMap.data | 0.000 | 0.001 | 0.000 | |
| read.snps.chiamo | 0 | 0 | 0 | |
| read.wtccc.signals | 0.000 | 0.001 | 0.000 | |
| row.summary | 0.130 | 0.009 | 0.140 | |
| single.snp.tests | 0.132 | 0.009 | 0.142 | |
| snp-class | 0.000 | 0.001 | 0.000 | |
| snp.cbind | 0.416 | 0.033 | 0.450 | |
| snp.cor | 0.293 | 0.011 | 0.305 | |
| snp.dprime-class | 0.110 | 0.008 | 0.118 | |
| snp.lhs.tests | 0.140 | 0.012 | 0.155 | |
| snp.matrix-class | 0.140 | 0.007 | 0.150 | |
| snp.pre | 0.125 | 0.010 | 0.135 | |
| snp.rhs.tests | 0.119 | 0.006 | 0.126 | |
| testdata | 0.141 | 0.008 | 0.150 | |
| xxt | 0.251 | 0.010 | 0.264 | |