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CHECK report for OCplus on malbec1

This page was generated on 2020-04-15 12:04:40 -0400 (Wed, 15 Apr 2020).

Package 1168/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OCplus 1.60.0
Alexander Ploner
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/OCplus
Branch: RELEASE_3_10
Last Commit: ddb509d
Last Changed Date: 2019-10-29 13:07:42 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OCplus
Version: 1.60.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:OCplus.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings OCplus_1.60.0.tar.gz
StartedAt: 2020-04-15 00:19:03 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:20:19 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 76.1 seconds
RetCode: 0
Status:  OK 
CheckDir: OCplus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:OCplus.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings OCplus_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/OCplus.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.60.0’
* 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 6.368  0.216   6.595
* 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-3.10-bioc/meat/OCplus.Rcheck/00check.log’
for details.



Installation output

OCplus.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL OCplus
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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
EOC0.6680.0280.699
FDR0.0040.0000.003
MAsim.smyth0.3160.0040.320
OCshow1.2560.0281.286
TOC0.2480.0040.250
average.fdr1.1840.0001.252
fdr1d0.5640.0000.563
fdr2d0.6880.0120.702
plot.FDR.result0.2840.0040.290
plot.fdr1d.result0.2480.0000.250
plot.fdr2d.result0.4280.0120.441
samplesize6.3680.2166.595
smooth1d0.0360.0120.049
summary.fdr.result0.8040.0040.808
tMixture3.4000.1883.594