BioC 3.5: CHECK report for SMITE on malbec2

Package: SMITE

Version: 1.4.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SMITE_1.4.1.tar.gz

StartedAt: 2017-08-16 02:22:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:25:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 223.7 seconds

RetCode: 0

Status:  OK

CheckDir: SMITE.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SMITE_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SMITE.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.1’
* 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 loading without being on the library search path ... 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 installed files from ‘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

* installing *source* package ‘SMITE’ ...
** R
** data
** inst
** preparing 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	0.092	0.000	0.094
SMITE-package	0.376	0.004	0.379
addShadowText	0.004	0.000	0.003
annotateExpression	0.244	0.004	0.246
annotateModification	0.000	0.000	0.001
convertGeneIds	1.644	0.064	1.710
curated_expression	0.048	0.000	0.048
extractExpression	0.784	0.000	0.784
extractGOseq	0.032	0.000	0.034
extractModification	1.688	0.012	1.699
extractModules	0.032	0.000	0.033
extractScores	0.032	0.000	0.034
genes_for_conversiontest	0.816	0.000	0.813
hg19_gene_bed	0.124	0.000	0.123
highScores	0.032	0.000	0.031
histone_h3k4me1	0.068	0.000	0.069
makePvalueAnnotation	0.812	0.008	0.819
makePvalueObject	0.064	0.000	0.064
methylationdata	0.060	0.000	0.061
normalizePval	0.032	0.000	0.033
plotCompareScores	1.616	0.012	1.630
plotDensityPval	0.064	0.008	0.070
plotModule	0.028	0.004	0.033
removeModification	0.068	0.000	0.068
runBioNet	0.032	0.000	0.032
runGOseq	0.032	0.004	0.037
runSpinglass	0.692	0.004	0.695
scorePval	0.028	0.004	0.032
stoufferTest	0.004	0.000	0.002
test_annotation_score_data	0.128	0.000	0.126