Package: SMITE

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMITE_1.11.1.tar.gz

StartedAt: 2019-04-09 05:37:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:43:51 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 384.9 seconds

RetCode: 0

Status:  OK

CheckDir: SMITE.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:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMITE_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SMITE.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.11.1’
* 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 ‘SMITE’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 SMITE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SMITE’ ...
** using staged installation
** R
** data
** 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 (SMITE)

name	user	system	elapsed
Reactome.Symbol.Igraph	0.126	0.029	0.155
SMITE-package	0.538	0.050	0.589
addShadowText	0.004	0.000	0.005
annotateExpression	0.276	0.019	0.295
annotateModification	0.001	0.000	0.001
convertGeneIds	3.754	0.347	4.118
curated_expression	0.046	0.005	0.051
extractExpression	0.184	0.012	0.197
extractGOseq	0.057	0.006	0.063
extractModification	1.346	0.123	1.468
extractModules	0.038	0.005	0.042
extractScores	0.057	0.006	0.063
genes_for_conversiontest	1.402	0.025	1.426
hg19_gene_bed	0.185	0.012	0.196
highScores	0.046	0.003	0.049
histone_h3k4me1	0.066	0.006	0.072
makePvalueAnnotation	1.089	0.104	1.192
makePvalueObject	0.083	0.011	0.095
methylationdata	0.081	0.011	0.091
normalizePval	0.056	0.006	0.062
plotCompareScores	0.718	0.031	0.750
plotDensityPval	0.079	0.009	0.089
plotModule	0.037	0.005	0.042
removeModification	0.087	0.015	0.101
runBioNet	0.054	0.006	0.060
runGOseq	0.389	0.010	0.398
runSpinglass	1.082	0.131	1.219
scorePval	0.040	0.006	0.046
stoufferTest	0.003	0.001	0.003
test_annotation_score_data	0.163	0.019	0.182