Package: SMITE

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2018-10-17 00:09:16 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:13:58 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 281.8 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SMITE.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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/3.5/Resources/library’
* installing *source* package ‘SMITE’ ...
** 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
* DONE (SMITE)

name	user	system	elapsed
Reactome.Symbol.Igraph	0.133	0.017	0.153
SMITE-package	0.504	0.034	0.545
addShadowText	0.005	0.001	0.005
annotateExpression	0.252	0.018	0.272
annotateModification	0.003	0.000	0.003
convertGeneIds	2.310	0.141	2.485
curated_expression	0.043	0.003	0.047
extractExpression	0.872	0.009	0.888
extractGOseq	0.045	0.003	0.048
extractModification	1.141	0.060	1.216
extractModules	0.038	0.003	0.041
extractScores	0.046	0.003	0.048
genes_for_conversiontest	1.245	0.015	1.269
hg19_gene_bed	0.156	0.007	0.168
highScores	0.052	0.002	0.057
histone_h3k4me1	0.099	0.007	0.108
makePvalueAnnotation	0.786	0.054	0.852
makePvalueObject	0.082	0.006	0.088
methylationdata	0.076	0.006	0.082
normalizePval	0.052	0.003	0.056
plotCompareScores	0.874	0.017	0.906
plotDensityPval	0.087	0.006	0.095
plotModule	0.054	0.003	0.058
removeModification	0.116	0.008	0.124
runBioNet	0.056	0.003	0.059
runGOseq	0.060	0.003	0.063
runSpinglass	0.848	0.053	0.913
scorePval	0.045	0.003	0.048
stoufferTest	0.004	0.000	0.004
test_annotation_score_data	0.099	0.007	0.107