BioC 3.6: CHECK report for SMITE on veracruz1

Package: SMITE

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SMITE_1.5.1.tar.gz

StartedAt: 2017-08-16 08:41:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:45:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 265.7 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 --no-vignettes --timings SMITE_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SMITE.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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	0.104	0.012	0.116
SMITE-package	0.397	0.027	0.432
addShadowText	0.004	0.000	0.004
annotateExpression	0.257	0.012	0.276
annotateModification	0.002	0.000	0.001
convertGeneIds	2.915	0.107	3.127
curated_expression	0.045	0.003	0.048
extractExpression	0.318	0.014	0.346
extractGOseq	0.042	0.004	0.045
extractModification	1.976	0.050	2.078
extractModules	0.032	0.002	0.034
extractScores	0.037	0.002	0.041
genes_for_conversiontest	1.214	0.008	1.253
hg19_gene_bed	0.145	0.008	0.158
highScores	0.039	0.001	0.041
histone_h3k4me1	0.069	0.010	0.079
makePvalueAnnotation	1.462	0.053	1.558
makePvalueObject	0.066	0.005	0.073
methylationdata	0.058	0.005	0.063
normalizePval	0.037	0.002	0.039
plotCompareScores	1.520	0.033	1.579
plotDensityPval	0.080	0.005	0.094
plotModule	0.034	0.002	0.037
removeModification	0.064	0.005	0.074
runBioNet	0.034	0.003	0.036
runGOseq	0.043	0.002	0.046
runSpinglass	0.929	0.040	1.001
scorePval	0.038	0.002	0.040
stoufferTest	0.002	0.000	0.002
test_annotation_score_data	0.121	0.005	0.127