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This page was generated on 2021-11-26 15:05:41 -0500 (Fri, 26 Nov 2021).

CHECK results for ACE on machv2

To the developers/maintainers of the ACE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ACE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 12/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACE 1.12.0  (landing page)
Jos B Poell
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/ACE
git_branch: RELEASE_3_14
git_last_commit: 543b422
git_last_commit_date: 2021-10-26 12:45:46 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ACE
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACE_1.12.0.tar.gz
StartedAt: 2021-11-25 13:37:00 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 13:40:59 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 238.9 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/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACE_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ACE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.12.0’
* 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 ... NOTE
squaremodel: no visible binding for global variable ‘cellularity’
Undefined global functions or variables:
  cellularity
* 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 LazyData ... 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 13.772  0.126  13.921
squaremodel        13.317  0.077  13.412
twosamplecompare    8.789  0.076   8.885
loopsquaremodel     6.442  0.055   6.512
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ACE.Rcheck/00check.log’
for details.



Installation output

ACE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ACE
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
ACEcall1.9200.5072.469
analyzegenomiclocations0.0300.0050.034
compresstemplate0.0830.0120.095
copyNumbersSegmented1.8140.1001.919
correlationmatrix0.1650.0100.176
forcesegmentsontemplate0.5780.0330.611
getadjustedsegments0.3130.0100.324
linkvariants0.0370.0030.040
loopsquaremodel6.4420.0556.512
objectsampletotemplate0.0070.0010.008
postanalysisloop000
runACE0.0010.0010.000
singlemodel1.0650.0161.083
singleplot1.5370.0241.564
squaremodel13.317 0.07713.412
squaremodelsummary13.772 0.12613.921
templatefromequalsegments0.0410.0020.043
twosamplecompare8.7890.0768.885