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CHECK report for siggenes on celaya2

This page was generated on 2019-10-16 12:44:45 -0400 (Wed, 16 Oct 2019).

Package 1516/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
siggenes 1.58.0
Holger Schwender
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/siggenes
Branch: RELEASE_3_9
Last Commit: 6950015
Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019)
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 [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: siggenes
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:siggenes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings siggenes_1.58.0.tar.gz
StartedAt: 2019-10-16 06:52:50 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:54:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 114.3 seconds
RetCode: 0
Status:  OK 
CheckDir: siggenes.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:siggenes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings siggenes_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/siggenes.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.58.0’
* 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 ‘siggenes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("get_stat_num_denum", ..., PACKAGE = "multtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/siggenes.Rcheck/00check.log’
for details.



Installation output

siggenes.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL siggenes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘siggenes’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘siggenes.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (siggenes)

Tests output


Example timings

siggenes.Rcheck/siggenes-Ex.timings

nameusersystemelapsed
EBAM-class0.0010.0000.001
SAM-class0.0010.0010.001
chisq.ebam0.0010.0010.001
chisq.stat0.0000.0010.001
delta.plot0.0000.0010.001
denspr0.0010.0000.001
ebam0.0010.0010.003
find.a00.0010.0010.001
help.ebam000
help.finda00.0010.0000.000
help.sam0.0000.0010.000
list.siggenes0.0010.0000.001
md.plot0.0000.0000.001
pi0.est0.0000.0010.001
qvalue.cal0.0000.0000.001
sam0.0010.0010.002
sam.plot20.0000.0000.001
trend.ebam0.0000.0000.001
trend.stat0.0000.0010.002