Package: SPLINTER

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SPLINTER_1.4.0.tar.gz

StartedAt: 2018-04-12 09:57:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:02:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 296.7 seconds

RetCode: 0

Status:  OK

CheckDir: SPLINTER.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 SPLINTER_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SPLINTER.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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            8.043  0.160   8.315
addEnsemblAnnotation 0.792  0.014   7.840
* 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	0.002	0.000	0.003
addEnsemblAnnotation	0.792	0.014	7.840
callPrimer3	0.001	0.000	0.001
checkPrimer	0.196	0.021	0.218
compatible_cds	0.001	0.001	0.002
compatible_tx	0.001	0.000	0.001
donor.m	0.001	0.001	0.002
eventOutcomeCompare	1.839	0.031	1.888
eventOutcomeTranslate	0.401	0.009	0.414
eventPlot	8.043	0.160	8.315
extendROI	0.498	0.002	0.504
extractSpliceEvents	0.024	0.000	0.024
extractSpliceSites	0.235	0.000	0.237
findCompatibleEvents	0.391	0.001	0.403
findCompatibleExon	0.212	0.001	0.214
findTX	0.008	0.000	0.007
getPCRsizes	3.872	0.168	4.132
getRegionDNA	0.328	0.007	0.349
insertRegion	0.087	0.001	0.088
makeROI	0.333	0.001	0.334
makeUniqueIDs	0.004	0.000	0.004
pcr_result1	0.002	0.001	0.003
plot_seqlogo	0.186	0.003	0.195
primers	0.001	0.000	0.003
psiPlot	0.972	0.004	1.000
region_minus_exon	0.002	0.001	0.002
roi	0.001	0.001	0.001
shapiroAcceptor	1.409	0.016	1.445
shapiroDonor	0.487	0.010	0.502
splice_data	0.001	0.001	0.002
splice_fasta	0.001	0.000	0.002
splitPCRhit	0.001	0.000	0.001
thecds	0.002	0.001	0.002
theexons	0.002	0.001	0.002
valid_cds	0.001	0.000	0.002
valid_tx	0.002	0.001	0.002