Package: SMITE

Version: 1.10.1

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_1.10.1.tar.gz

StartedAt: 2019-04-16 02:52:32 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:57:14 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 282.0 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_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SMITE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.1’
* 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/3.5/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	0.109	0.016	0.127
SMITE-package	0.508	0.042	0.572
addShadowText	0.004	0.000	0.004
annotateExpression	0.250	0.015	0.267
annotateModification	0	0	0
convertGeneIds	2.377	0.142	2.540
curated_expression	0.059	0.004	0.063
extractExpression	0.817	0.010	0.829
extractGOseq	0.034	0.003	0.037
extractModification	0.848	0.062	0.916
extractModules	0.032	0.003	0.035
extractScores	0.033	0.002	0.036
genes_for_conversiontest	1.102	0.011	1.119
hg19_gene_bed	0.133	0.005	0.139
highScores	0.031	0.002	0.033
histone_h3k4me1	0.066	0.004	0.069
makePvalueAnnotation	0.656	0.053	0.713
makePvalueObject	0.087	0.006	0.093
methylationdata	0.054	0.003	0.057
normalizePval	0.032	0.002	0.034
plotCompareScores	0.425	0.016	0.441
plotDensityPval	0.067	0.003	0.071
plotModule	0.032	0.002	0.035
removeModification	0.063	0.005	0.067
runBioNet	0.032	0.002	0.035
runGOseq	0.201	0.004	0.206
runSpinglass	0.583	0.049	0.634
scorePval	0.069	0.005	0.075
stoufferTest	0.002	0.000	0.002
test_annotation_score_data	0.078	0.003	0.082