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CHECK report for XCIR on merida1

This page was generated on 2020-04-15 12:49:31 -0400 (Wed, 15 Apr 2020).

Package 1809/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XCIR 1.0.0
Renan Sauteraud
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/XCIR
Branch: RELEASE_3_10
Last Commit: c20f64b
Last Changed Date: 2019-10-29 13:11:42 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
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: XCIR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XCIR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XCIR_1.0.0.tar.gz
StartedAt: 2020-04-15 06:28:44 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:35:00 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 376.5 seconds
RetCode: 0
Status:  OK 
CheckDir: XCIR.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:XCIR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XCIR_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/XCIR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XCIR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XCIR’ version ‘1.0.0’
* 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 ‘XCIR’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user  system elapsed
betaBinomXI  73.860  81.201  18.182
getXCIstate  53.329 101.248  19.309
plotQC       60.810  93.004  17.931
sample_clean 56.923  96.506  18.757
readRNASNPs   6.137   4.497   7.109
annotateX     5.996   4.076   7.966
getGenicDP    4.600   5.232   5.778
readVCF4      4.224   5.447   5.812
addAnno       6.391   3.200   5.524
* 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: OK


Installation output

XCIR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL XCIR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘XCIR’ ...
** using staged installation
** R
** 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 (XCIR)

Tests output


Example timings

XCIR.Rcheck/XCIR-Ex.timings

nameusersystemelapsed
BetaConversion0.0000.0000.001
addAnno6.3913.2005.524
annotateX5.9964.0767.966
betaBinomXI73.86081.20118.182
consensusXCI1.1961.4890.347
getGenicDP4.6005.2325.778
getXCIstate 53.329101.248 19.309
mart_genes1.3561.1094.533
plotQC60.81093.00417.931
readRNASNPs6.1374.4977.109
readVCF44.2245.4475.812
readXCI0.0070.0070.002
sample_clean56.92396.50618.757