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CHECK report for MADSEQ on malbec2

This page was generated on 2019-04-09 11:46:15 -0400 (Tue, 09 Apr 2019).

Package 889/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MADSEQ 1.9.0
Yu Kong
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MADSEQ
Branch: master
Last Commit: 5bfec4f
Last Changed Date: 2018-10-30 11:54:36 -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  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: MADSEQ
Version: 1.9.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MADSEQ.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MADSEQ_1.9.0.tar.gz
StartedAt: 2019-04-09 01:39:40 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:44:41 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 301.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MADSEQ.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MADSEQ.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MADSEQ_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MADSEQ.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 ‘MADSEQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MADSEQ’ version ‘1.9.0’
* 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 ‘MADSEQ’ 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
removeRE: no visible global function definition for ‘seqlevelsStyle<-’
Undefined global functions or variables:
  seqlevelsStyle<-
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCoverage 9.612  0.175   9.906
runMadSeq         7.840  0.008   7.860
* 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/MADSEQ.Rcheck/00check.log’
for details.



Installation output

MADSEQ.Rcheck/00install.out

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

Tests output


Example timings

MADSEQ.Rcheck/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.0180.0000.019
deltaBIC0.0060.0000.006
normalizeCoverage9.6120.1759.906
plotFraction0.0160.0000.016
plotMadSeq0.0300.0000.029
plotMixture0.0160.0040.019
posterior0.1130.1160.229
prepareCoverageGC1.7980.0281.827
prepareHetero1.8600.0041.946
runMadSeq7.8400.0087.860
summary-method0.0190.0000.019