Package: SMITE

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2020-01-16 09:02:49 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:10:10 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 441.2 seconds

RetCode: 0

Status:  OK

CheckDir: SMITE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SMITE.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SMITE’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SMITE)

name	user	system	elapsed
Reactome.Symbol.Igraph	0.134	0.031	0.165
SMITE-package	0.585	0.059	0.643
addShadowText	0.004	0.001	0.005
annotateExpression	0.292	0.027	0.319
annotateModification	0.001	0.001	0.001
convertGeneIds	2.909	0.301	3.218
curated_expression	0.065	0.006	0.072
extractExpression	1.276	0.016	1.294
extractGOseq	0.057	0.006	0.063
extractModification	1.708	0.139	1.848
extractModules	0.056	0.007	0.063
extractScores	0.055	0.006	0.062
genes_for_conversiontest	1.571	0.024	1.595
hg19_gene_bed	0.209	0.016	0.226
highScores	0.052	0.006	0.058
histone_h3k4me1	0.164	0.024	0.187
makePvalueAnnotation	1.256	0.094	1.353
makePvalueObject	0.072	0.008	0.081
methylationdata	0.086	0.009	0.095
normalizePval	0.058	0.006	0.065
plotCompareScores	0.912	0.045	0.957
plotDensityPval	0.108	0.010	0.119
plotModule	0.050	0.005	0.056
removeModification	0.090	0.018	0.108
runBioNet	0.059	0.007	0.065
runGOseq	0.063	0.007	0.070
runSpinglass	1.028	0.119	1.181
scorePval	0.056	0.007	0.062
stoufferTest	0.002	0.001	0.002
test_annotation_score_data	0.102	0.012	0.115