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CHECK report for ACE on merida1

This page was generated on 2019-04-16 12:11:08 -0400 (Tue, 16 Apr 2019).

Package 12/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACE 1.0.0
Jos B Poell
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ACE
Branch: RELEASE_3_8
Last Commit: a7e7ae6
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 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: ACE
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACE_1.0.0.tar.gz
StartedAt: 2019-04-15 22:15:45 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:18:57 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 192.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ACE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACE_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ACE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACE/DESCRIPTION’ ... OK
* this is package ‘ACE’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ACE’ 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: ‘QDNAseq:::sdDiffTrim’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* 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 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
squaremodel        16.262  0.216  17.923
squaremodelsummary 13.882  0.159  14.152
loopsquaremodel     5.700  0.108   5.827
twosamplecompare    5.432  0.043   5.515
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/ACE.Rcheck/00check.log’
for details.



Installation output

ACE.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ACE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ACE’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (ACE)

Tests output


Example timings

ACE.Rcheck/ACE-Ex.timings

nameusersystemelapsed
ACEcall2.3260.4162.759
analyzegenomiclocations0.0440.0050.049
compresstemplate0.0680.0010.070
copyNumbersSegmented1.0110.0341.055
correlationmatrix0.0810.0030.084
getadjustedsegments0.2310.0060.239
linkvariants0.0240.0010.025
loopsquaremodel5.7000.1085.827
objectsampletotemplate0.0100.0020.011
postanalysisloop000
runACE000
singlemodel1.4020.0211.434
singleplot1.7740.0141.808
squaremodel16.262 0.21617.923
squaremodelsummary13.882 0.15914.152
templatefromequalsegments0.0320.0030.034
twosamplecompare5.4320.0435.515