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CHECK report for OCplus on malbec2

This page was generated on 2019-10-16 11:56:02 -0400 (Wed, 16 Oct 2019).

Package 1120/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OCplus 1.58.0
Alexander Ploner
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/OCplus
Branch: RELEASE_3_9
Last Commit: b1f7e0d
Last Changed Date: 2019-05-02 11:53:06 -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: OCplus
Version: 1.58.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OCplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OCplus_1.58.0.tar.gz
StartedAt: 2019-10-16 03:36:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:37:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 75.5 seconds
RetCode: 0
Status:  OK 
CheckDir: OCplus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OCplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OCplus_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/OCplus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ 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 ‘OCplus’ 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.FDR.result plot.fdr1d.result plot.fdr2d.result
  summary.fdr.result
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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
samplesize 6.62  0.212   6.832
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/OCplus.Rcheck/00check.log’
for details.



Installation output

OCplus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL OCplus
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘OCplus’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OCplus)

Tests output


Example timings

OCplus.Rcheck/OCplus-Ex.timings

nameusersystemelapsed
EOC0.5920.0200.613
FDR0.0030.0000.004
MAsim.smyth0.1820.0040.186
OCshow1.0690.0081.077
TOC0.2420.0120.253
average.fdr1.3940.0041.427
fdr1d0.4510.0000.450
fdr2d0.6270.0050.631
plot.FDR.result0.0960.0030.099
plot.fdr1d.result0.7670.0080.774
plot.fdr2d.result0.4480.0080.456
samplesize6.6200.2126.832
smooth1d0.0440.0040.048
summary.fdr.result0.3590.0080.366
tMixture3.6330.1363.770