Package: SMITE

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2019-10-16 07:00:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:06:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 386.1 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SMITE.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 ‘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	0.180	0.033	0.213
SMITE-package	0.640	0.066	0.707
addShadowText	0.004	0.001	0.005
annotateExpression	1.069	0.025	1.096
annotateModification	0.001	0.001	0.001
convertGeneIds	2.739	0.293	3.038
curated_expression	0.060	0.007	0.067
extractExpression	0.235	0.019	0.254
extractGOseq	0.168	0.013	0.181
extractModification	1.440	0.112	1.552
extractModules	0.062	0.007	0.068
extractScores	1.072	0.017	1.089
genes_for_conversiontest	1.741	0.024	1.765
hg19_gene_bed	0.205	0.014	0.219
highScores	0.060	0.004	0.064
histone_h3k4me1	0.082	0.012	0.094
makePvalueAnnotation	0.736	0.093	0.829
makePvalueObject	0.140	0.028	0.168
methylationdata	0.076	0.011	0.088
normalizePval	0.056	0.004	0.060
plotCompareScores	0.780	0.034	0.817
plotDensityPval	0.117	0.014	0.132
plotModule	0.062	0.005	0.068
removeModification	0.072	0.016	0.088
runBioNet	0.062	0.006	0.067
runGOseq	0.505	0.017	0.522
runSpinglass	0.728	0.099	0.827
scorePval	0.067	0.006	0.072
stoufferTest	0.003	0.000	0.003
test_annotation_score_data	0.113	0.012	0.126