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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 337/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chopsticks 1.73.0  (landing page)
Hin-Tak Leung
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/chopsticks
git_branch: devel
git_last_commit: 8e3687b
git_last_commit_date: 2024-12-04 17:57:33 -0500 (Wed, 04 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for chopsticks on lconway

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.

raw results


Summary

Package: chopsticks
Version: 1.73.0
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_1.73.0.tar.gz
StartedAt: 2024-12-23 19:30:00 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:31:10 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 69.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chopsticks.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### 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_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.73.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chopsticks’ can be installed ... WARNING
Found the following significant warnings:
  glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is  5.2Mb
  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/4.5-x86_64/Resources/library/chopsticks/libs/chopsticks.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
File ‘chopsticks/libs/chopsticks.so’:
  Found non-API calls to R: ‘R_data_class’, ‘SET_S4_OBJECT’

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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00check.log’
for details.


Installation output

chopsticks.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘chopsticks’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c adler32.c -o adler32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bind.c -o bind.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c compress.c -o compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c crc32.c -o crc32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c deflate.c -o deflate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c force_hom.c -o force_hom.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c glm_test_R.c -o glm_test_R.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gzio.c -o gzio.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hash_index.c -o hash_index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ibs.c -o ibs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c in.c -o in.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c infback.c -o infback.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inffast.c -o inffast.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inflate.c -o inflate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inftrees.c -o inftrees.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c input.c -o input.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inputNew.c -o inputNew.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c input_unsorted.c -o input_unsorted.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ld_graphic_eps.c -o ld_graphic_eps.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ld_with.c -o ld_with.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mla.c -o mla.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c outdata.c -o outdata.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pairwise_linkage.c -o pairwise_linkage.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_chiamo.c -o read_chiamo.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_hapmap.c -o read_hapmap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_pedfile.c -o read_pedfile.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_signals.c -o read_signals.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readped.c -o readped.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sdfpw.c -o sdfpw.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c single_snp_tests.c -o single_snp_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snp_summary.c -o snp_summary.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snpmpy.c -o snpmpy.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c solve_cubic.c -o solve_cubic.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c solve_quadratic.c -o solve_quadratic.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c structure.c -o structure.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c trees.c -o trees.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c uncompr.c -o uncompr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c zutil.c -o zutil.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.5-x86_64/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)

Tests output


Example timings

chopsticks.Rcheck/chopsticks-Ex.timings

nameusersystemelapsed
X.snp-class0.0940.0160.111
X.snp.matrix-class0.0950.0080.105
epsout.ld.snp0.1220.0160.145
for.exercise0.6030.0320.641
ibs.stats0.0930.0090.103
ibsCount0.2540.0120.270
ibsDist0.1530.0080.162
ld.snp0.0930.0060.100
ld.with0.0880.0080.098
pair.result.ld.snp0.0840.0060.092
plot.snp.dprime0.1880.0220.211
qq.chisq000
read.HapMap.data0.0000.0010.001
read.snps.chiamo0.0000.0000.001
read.wtccc.signals000
row.summary0.0780.0050.083
single.snp.tests0.0940.0090.105
snp-class000
snp.cbind0.2860.0320.320
snp.cor0.2700.0060.278
snp.dprime-class0.0670.0070.074
snp.lhs.tests0.0910.0150.106
snp.matrix-class0.1010.0060.108
snp.pre0.0760.0050.082
snp.rhs.tests0.0770.0040.082
testdata0.1050.0170.122
xxt0.2020.0070.210