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This page was generated on 2024-07-16 17:43 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 2225/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twilight 1.80.0  (landing page)
Stefanie Scheid
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/twilight
git_branch: RELEASE_3_19
git_last_commit: 9e9d406
git_last_commit_date: 2024-04-30 10:13:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for twilight on kjohnson1

To the developers/maintainers of the twilight package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/twilight.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: twilight
Version: 1.80.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twilight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twilight_1.80.0.tar.gz
StartedAt: 2024-07-16 12:18:13 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 12:18:52 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 38.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: twilight.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twilight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twilight_1.80.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/twilight.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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twilight/DESCRIPTION’ ... OK
* this is package ‘twilight’ version ‘1.80.0’
* 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 ‘twilight’ can be installed ... WARNING
Found the following significant warnings:
  sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/twilight.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 ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘stats’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

twilight: no visible global function definition for ‘makeCluster’
twilight: no visible global function definition for ‘clusterEvalQ’
twilight: no visible binding for '<<-' assignment to
  ‘.twilight.lambda.xxx’
twilight: no visible binding for '<<-' assignment to
  ‘.twilight.pval.xxx’
twilight: no visible binding for '<<-' assignment to
  ‘.twilight.score.xxx’
twilight: no visible global function definition for ‘clusterExport’
twilight: no visible global function definition for ‘parCapply’
twilight: no visible binding for global variable ‘.twilight.lambda.xxx’
twilight: no visible binding for global variable ‘.twilight.pval.xxx’
twilight: no visible binding for global variable ‘.twilight.score.xxx’
twilight: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  .twilight.lambda.xxx .twilight.pval.xxx .twilight.score.xxx
  clusterEvalQ clusterExport makeCluster parCapply stopCluster
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/twilight/libs/twilight.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/twilight.Rcheck/00check.log’
for details.


Installation output

twilight.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘twilight’ ...
** 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 confidence.line.c -o confidence.line.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 correlation.c -o correlation.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 kstest.c -o kstest.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 sep.c -o sep.o
sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
          ix[randnum]=fabs(1-ix[randnum]);
                      ^
sep.c:70:16: note: use function 'abs' instead
          ix[randnum]=fabs(1-ix[randnum]);
                      ^~~~
                      abs
sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
              ix[randnum]=fabs(1-ix[randnum]);
                          ^
sep.c:97:20: note: use function 'abs' instead
              ix[randnum]=fabs(1-ix[randnum]);
                          ^~~~
                          abs
sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
      ix[randnum]=fabs(1-ix[randnum]);
                  ^
sep.c:116:19: note: use function 'abs' instead
      ix[randnum]=fabs(1-ix[randnum]);
                  ^~~~
                  abs
sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
          ix[randnum]=fabs(1-ix[randnum]);
                      ^
sep.c:143:16: note: use function 'abs' instead
          ix[randnum]=fabs(1-ix[randnum]);
                      ^~~~
                      abs
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 twosample.perm.c -o twosample.perm.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 twosample.single.c -o twosample.single.o
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 twilight.so confidence.line.o correlation.o kstest.o sep.o twosample.perm.o twosample.single.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-twilight/00new/twilight/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded 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 (twilight)

Tests output


Example timings

twilight.Rcheck/twilight-Ex.timings

nameusersystemelapsed
plot.twilight0.2830.0210.305
print.twilight0.0620.0030.066
twilight0.5060.0220.529
twilight.combi0.0030.0010.004
twilight.filtering0.0000.0010.000
twilight.pval0.4180.0160.434
twilight.teststat0.0040.0010.004