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CHECK report for twilight on malbec2

This page was generated on 2019-04-09 11:23:44 -0400 (Tue, 09 Apr 2019).

Package 1654/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twilight 1.59.0
Stefanie Scheid
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/twilight
Branch: master
Last Commit: 1b3c8da
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: twilight
Version: 1.59.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:twilight.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings twilight_1.59.0.tar.gz
StartedAt: 2019-04-09 04:12:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:13:34 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 38.0 seconds
RetCode: 0
Status:  OK 
CheckDir: twilight.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:twilight.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings twilight_1.59.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/twilight.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twilight/DESCRIPTION’ ... OK
* this is package ‘twilight’ version ‘1.59.0’
* 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 ... OK
* 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 R 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.twilight print.twilight
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ‘/home/biocbuild/bbs-3.9-bioc/R/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. 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/twilight.Rcheck/00check.log’
for details.



Installation output

twilight.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL twilight
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘twilight’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c confidence.line.c -o confidence.line.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c correlation.c -o correlation.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c kstest.c -o kstest.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c sep.c -o sep.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c twosample.perm.c -o twosample.perm.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c twosample.single.c -o twosample.single.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o twilight.so confidence.line.o correlation.o kstest.o sep.o twosample.perm.o twosample.single.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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.twilight0.1720.0070.239
print.twilight0.0580.0040.065
twilight0.1500.0080.161
twilight.combi0.0040.0000.004
twilight.filtering0.0000.0000.001
twilight.pval0.1060.0000.132
twilight.teststat0.0050.0000.005