Package: SMITE

Version: 1.10.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SMITE_1.10.1.tar.gz

StartedAt: 2019-04-16 03:09:33 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:13:47 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 253.8 seconds

RetCode: 0

Status:  OK

CheckDir: SMITE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SMITE_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SMITE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.1’
* 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 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	0.120	0.004	0.140
SMITE-package	0.600	0.020	0.623
addShadowText	0.000	0.004	0.004
annotateExpression	0.268	0.000	0.270
annotateModification	0	0	0
convertGeneIds	2.956	0.120	3.082
curated_expression	0.068	0.000	0.067
extractExpression	0.228	0.000	0.229
extractGOseq	0.048	0.000	0.051
extractModification	1.096	0.004	1.105
extractModules	0.052	0.000	0.053
extractScores	0.056	0.000	0.054
genes_for_conversiontest	1.264	0.000	1.267
hg19_gene_bed	0.212	0.000	0.215
highScores	0.052	0.000	0.054
histone_h3k4me1	0.124	0.000	0.123
makePvalueAnnotation	0.780	0.012	0.791
makePvalueObject	0.088	0.000	0.089
methylationdata	0.084	0.004	0.088
normalizePval	0.044	0.004	0.048
plotCompareScores	0.564	0.004	0.569
plotDensityPval	0.108	0.000	0.104
plotModule	0.092	0.000	0.093
removeModification	0.092	0.000	0.093
runBioNet	0.048	0.000	0.048
runGOseq	0.304	0.000	0.303
runSpinglass	0.932	0.012	0.947
scorePval	0.052	0.000	0.056
stoufferTest	0.000	0.000	0.002
test_annotation_score_data	0.108	0.000	0.106