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CHECK report for ACE on malbec1

This page was generated on 2020-04-15 12:14:30 -0400 (Wed, 15 Apr 2020).

Package 12/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACE 1.4.0
Jos B Poell
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ACE
Branch: RELEASE_3_10
Last Commit: 246b8d7
Last Changed Date: 2019-10-29 13:11:17 -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: ACE
Version: 1.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ACE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ACE_1.4.0.tar.gz
StartedAt: 2020-04-15 05:54:17 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:57:20 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 182.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ACE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ACE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ACE_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ACE.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 ‘ACE/DESCRIPTION’ ... OK
* this is package ‘ACE’ version ‘1.4.0’
* 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        11.920  0.024  11.970
squaremodelsummary 10.952  0.028  11.021
twosamplecompare    6.092  0.008   6.111
loopsquaremodel     6.052  0.028   6.107
* 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/ACE.Rcheck/00check.log’
for details.



Installation output

ACE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ACE
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ACE’ ...
** 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 (ACE)

Tests output


Example timings

ACE.Rcheck/ACE-Ex.timings

nameusersystemelapsed
ACEcall2.1280.2242.354
analyzegenomiclocations0.0280.0000.025
compresstemplate0.0720.0000.072
copyNumbersSegmented1.2920.0401.334
correlationmatrix0.1480.0000.146
forcesegmentsontemplate0.5600.0040.568
getadjustedsegments0.2880.0000.288
linkvariants0.0280.0000.028
loopsquaremodel6.0520.0286.107
objectsampletotemplate0.0120.0000.012
postanalysisloop000
runACE0.0000.0000.001
singlemodel1.3360.0121.350
singleplot1.8480.0081.858
squaremodel11.920 0.02411.970
squaremodelsummary10.952 0.02811.021
templatefromequalsegments0.0360.0000.034
twosamplecompare6.0920.0086.111