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CHECK report for RNASeqR on malbec1

This page was generated on 2019-04-16 11:53:50 -0400 (Tue, 16 Apr 2019).

Package 1332/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNASeqR 1.0.3
Kuan-Hao Chao
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RNASeqR
Branch: RELEASE_3_8
Last Commit: ba9f675
Last Changed Date: 2018-12-04 12:05:44 -0400 (Tue, 04 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: RNASeqR
Version: 1.0.3
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RNASeqR_1.0.3.tar.gz
StartedAt: 2019-04-16 02:42:04 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:47:55 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 351.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RNASeqR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RNASeqR_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RNASeqR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNASeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNASeqR’ version ‘1.0.3’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RNASeqR’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignmentPlot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  value
* 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 files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
RNASeqRParam-constructor 0.668   1.58   5.347
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RNASeqR.Rcheck/00check.log’
for details.



Installation output

RNASeqR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RNASeqR
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RNASeqR’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RNASeqR)

Tests output


Example timings

RNASeqR.Rcheck/RNASeqR-Ex.timings

nameusersystemelapsed
CheckToolAll0.0040.0000.002
RNASeqDifferentialAnalysis0.0000.0000.002
RNASeqDifferentialAnalysis_CMD0.0000.0000.002
RNASeqEnvironmentSet0.0000.0000.002
RNASeqEnvironmentSet_CMD0.0040.0000.002
RNASeqGoKegg0.0000.0000.002
RNASeqGoKegg_CMD0.0000.0000.002
RNASeqQualityAssessment0.0000.0000.002
RNASeqQualityAssessment_CMD0.0000.0040.002
RNASeqRParam-class0.0000.0040.003
RNASeqRParam-constructor0.6681.5805.347
RNASeqReadProcess0.0000.0000.003
RNASeqReadProcess_CMD0.0000.0000.002
yeast0.0040.0000.002