Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ACE on merida1

This page was generated on 2021-05-06 12:34:15 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ACE package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 12/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACE 1.8.0  (landing page)
Jos B Poell
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ACE
Branch: RELEASE_3_12
Last Commit: 6a04454
Last Changed Date: 2020-10-27 11:37:13 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ACE
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2021-05-05 23:02:56 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:06:27 -0400 (Wed, 05 May 2021)
EllapsedTime: 210.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ACE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ACE.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACE/DESCRIPTION’ ... OK
* this is package ‘ACE’ version ‘1.8.0’
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
squaremodelsummary 10.292  0.085  10.394
squaremodel         9.842  0.114   9.970
twosamplecompare    7.855  0.056   7.924
loopsquaremodel     4.964  0.053   5.023
* 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-3.12-bioc/meat/ACE.Rcheck/00check.log’
for details.



Installation output

ACE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ACE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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
ACEcall2.1570.7432.951
analyzegenomiclocations0.0360.0020.037
compresstemplate0.0840.0030.087
copyNumbersSegmented1.2500.0411.296
correlationmatrix0.1420.0030.145
forcesegmentsontemplate0.5350.0080.544
getadjustedsegments0.2420.0070.250
linkvariants0.0370.0020.039
loopsquaremodel4.9640.0535.023
objectsampletotemplate0.0080.0010.009
postanalysisloop000
runACE000
singlemodel0.8040.0270.832
singleplot1.2540.0231.279
squaremodel9.8420.1149.970
squaremodelsummary10.292 0.08510.394
templatefromequalsegments0.0440.0040.049
twosamplecompare7.8550.0567.924