BioC 3.5: CHECK report for SMITE on veracruz2

Package: SMITE

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SMITE_1.4.1.tar.gz

StartedAt: 2017-10-18 09:11:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:16:32 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 283.7 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SMITE.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.1’
* 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 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	0.084	0.008	0.094
SMITE-package	0.333	0.021	0.360
addShadowText	0.003	0.001	0.002
annotateExpression	0.222	0.010	0.243
annotateModification	0.001	0.000	0.001
convertGeneIds	2.210	0.116	2.401
curated_expression	0.554	0.006	0.576
extractExpression	0.309	0.011	0.327
extractGOseq	0.036	0.003	0.039
extractModification	1.982	0.074	2.103
extractModules	0.062	0.003	0.067
extractScores	0.039	0.003	0.044
genes_for_conversiontest	1.261	0.016	1.304
hg19_gene_bed	0.178	0.010	0.194
highScores	0.037	0.002	0.039
histone_h3k4me1	0.082	0.010	0.095
makePvalueAnnotation	1.611	0.059	1.758
makePvalueObject	0.067	0.010	0.078
methylationdata	0.061	0.016	0.079
normalizePval	0.062	0.003	0.066
plotCompareScores	1.630	0.035	1.722
plotDensityPval	0.083	0.005	0.093
plotModule	0.032	0.002	0.035
removeModification	0.068	0.007	0.076
runBioNet	0.040	0.002	0.051
runGOseq	0.064	0.003	0.068
runSpinglass	0.988	0.041	1.062
scorePval	0.041	0.002	0.045
stoufferTest	0.002	0.000	0.003
test_annotation_score_data	0.138	0.005	0.148