BioC 3.6: CHECK report for SPLINTER on malbec1

Package: SPLINTER

Version: 1.3.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SPLINTER_1.3.0.tar.gz

StartedAt: 2017-08-16 02:36:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:40:28 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 263.1 seconds

RetCode: 0

Status:  OK

CheckDir: SPLINTER.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SPLINTER_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SPLINTER.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 ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.3.0’
* 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 ‘SPLINTER’ 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
Examples with CPU or elapsed time > 5s
           user system elapsed
eventPlot 6.316  0.016   6.338
* 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 ‘SPLINTER’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SPLINTER)

name	user	system	elapsed
acceptor.m	0.000	0.000	0.002
addEnsemblAnnotation	0.316	0.012	4.151
callPrimer3	0	0	0
checkPrimer	0.816	0.000	0.816
compatible_cds	0.000	0.000	0.002
compatible_tx	0.004	0.000	0.001
donor.m	0.000	0.000	0.001
eventOutcomeCompare	1.972	0.016	2.008
eventOutcomeTranslate	0.376	0.004	0.381
eventPlot	6.316	0.016	6.338
extendROI	0.420	0.004	0.424
extractSpliceEvents	0.024	0.000	0.023
extractSpliceSites	0.196	0.000	0.193
findCompatibleEvents	0.296	0.000	0.296
findCompatibleExon	0.168	0.000	0.169
findTX	0.008	0.000	0.006
getPCRsizes	3.144	0.040	3.429
getRegionDNA	0.332	0.000	0.335
insertRegion	0.076	0.000	0.076
makeROI	0.244	0.000	0.248
makeUniqueIDs	0.000	0.000	0.002
pcr_result1	0.004	0.000	0.001
plot_seqlogo	0.132	0.000	0.131
primers	0.000	0.000	0.001
psiPlot	1.360	0.000	1.359
region_minus_exon	0.000	0.000	0.001
roi	0.000	0.000	0.001
shapiroAcceptor	0.720	0.004	0.760
shapiroDonor	0.436	0.004	0.437
splice_data	0.000	0.000	0.001
splice_fasta	0.000	0.000	0.001
splitPCRhit	0.004	0.000	0.001
thecds	0.000	0.000	0.001
theexons	0.004	0.000	0.001
valid_cds	0.000	0.000	0.001
valid_tx	0.004	0.000	0.002