Package: XCIR

Version: 1.1.0

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_1.1.0.tar.gz

StartedAt: 2020-01-16 09:53:50 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:01:35 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 464.6 seconds

RetCode: 0

Status:  OK

CheckDir: XCIR.Rcheck

Warnings: 0

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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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/XCIR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.1.0’
* 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 (user + system) or elapsed time > 5s
                user system elapsed
getXCIstate  140.556 22.772  16.642
sample_clean 141.766 13.367  15.092
betaBinomXI   84.795 67.304  19.853
plotQC        74.648 70.562  19.856
readRNASNPs   10.661  0.723   5.552
addAnno        7.991  2.541   8.126
annotateX      6.028  4.275   5.954
readVCF4       8.880  1.352   5.959
getGenicDP     4.195  4.652   7.298
mart_genes     1.831  0.933   7.858
* 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

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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/4.0/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)

name	user	system	elapsed
BetaConversion	0.001	0.001	0.001
addAnno	7.991	2.541	8.126
annotateX	6.028	4.275	5.954
betaBinomXI	84.795	67.304	19.853
consensusXCI	0.329	0.689	0.131
getGenicDP	4.195	4.652	7.298
getXCIstate	140.556	22.772	16.642
mart_genes	1.831	0.933	7.858
plotQC	74.648	70.562	19.856
readRNASNPs	10.661	0.723	5.552
readVCF4	8.880	1.352	5.959
readXCI	0.002	0.001	0.004
sample_clean	141.766	13.367	15.092