Package: SPLINTER

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPLINTER_1.8.1.tar.gz

StartedAt: 2019-04-16 02:57:06 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:02:51 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 345.0 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 --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPLINTER_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SPLINTER.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* package encoding: UTF-8
* 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 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
Examples with CPU or elapsed time > 5s
                       user system elapsed
eventPlot            12.254  0.345  12.866
getPCRsizes           4.963  0.220   5.315
addEnsemblAnnotation  0.369  0.026  12.598
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SPLINTER
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SPLINTER’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
* DONE (SPLINTER)

name	user	system	elapsed
acceptor.m	0.003	0.001	0.004
addEnsemblAnnotation	0.369	0.026	12.598
callPrimer3	0	0	0
checkPrimer	0.119	0.012	0.131
compatible_cds	0.002	0.001	0.003
compatible_tx	0.001	0.002	0.004
donor.m	0.002	0.001	0.003
eventOutcomeCompare	1.693	0.051	1.757
eventOutcomeTranslate	0.509	0.008	0.521
eventPlot	12.254	0.345	12.866
extendROI	0.920	0.029	0.960
extractSpliceEvents	0.005	0.000	0.006
extractSpliceSites	0.096	0.001	0.097
findCompatibleEvents	0.419	0.001	0.421
findCompatibleExon	0.256	0.000	0.260
findTX	0.008	0.000	0.012
getPCRsizes	4.963	0.220	5.315
getRegionDNA	0.376	0.008	0.385
insertRegion	0.168	0.001	0.170
makeROI	0.309	0.001	0.311
makeUniqueIDs	0.003	0.000	0.003
pcr_result1	0.001	0.001	0.002
plot_seqlogo	0.058	0.003	0.062
primers	0.002	0.001	0.003
psiPlot	0.311	0.003	0.316
region_minus_exon	0.002	0.001	0.002
roi	0.001	0.000	0.003
shapiroAcceptor	0.556	0.018	0.580
shapiroDonor	0.474	0.010	0.490
splice_data	0.002	0.001	0.002
splice_fasta	0.001	0.001	0.003
splitPCRhit	0.001	0.000	0.001
thecds	0.001	0.001	0.001
theexons	0.002	0.001	0.002
valid_cds	0.002	0.001	0.002
valid_tx	0.001	0.001	0.002