Package: SPLINTER

Version: 1.6.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SPLINTER_1.6.0.tar.gz

StartedAt: 2018-10-16 03:58:08 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 04:02:08 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 240.2 seconds

RetCode: 0

Status:  OK

CheckDir: SPLINTER.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SPLINTER_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SPLINTER.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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 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 ... NOTE
metaremove: no visible global function definition for 'is'
metaremove: no visible global function definition for 'endoapply'
Undefined global functions or variables:
  endoapply is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU or elapsed time > 5s
                      user system elapsed
eventPlot            8.644  0.052   8.729
addEnsemblAnnotation 0.248  0.008  25.083
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/SPLINTER.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SPLINTER
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘SPLINTER’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (SPLINTER)

name	user	system	elapsed
acceptor.m	0.004	0.000	0.002
addEnsemblAnnotation	0.248	0.008	25.083
callPrimer3	0.000	0.000	0.001
checkPrimer	0.116	0.000	0.117
compatible_cds	0.004	0.000	0.002
compatible_tx	0.004	0.000	0.002
donor.m	0.000	0.000	0.001
eventOutcomeCompare	1.224	0.052	1.291
eventOutcomeTranslate	0.316	0.004	0.319
eventPlot	8.644	0.052	8.729
extendROI	0.512	0.000	0.514
extractSpliceEvents	0.004	0.000	0.003
extractSpliceSites	0.076	0.000	0.076
findCompatibleEvents	0.272	0.000	0.273
findCompatibleExon	0.168	0.000	0.166
findTX	0.004	0.000	0.005
getPCRsizes	3.056	0.092	3.323
getRegionDNA	0.212	0.008	0.221
insertRegion	0.136	0.000	0.135
makeROI	0.236	0.000	0.234
makeUniqueIDs	0.004	0.000	0.002
pcr_result1	0.000	0.000	0.001
plot_seqlogo	0.044	0.000	0.041
primers	0.000	0.000	0.001
psiPlot	0.232	0.000	0.230
region_minus_exon	0.000	0.000	0.001
roi	0.004	0.000	0.001
shapiroAcceptor	0.448	0.004	0.489
shapiroDonor	0.560	0.008	0.568
splice_data	0.000	0.000	0.002
splice_fasta	0.004	0.000	0.002
splitPCRhit	0.004	0.000	0.002
thecds	0.000	0.000	0.002
theexons	0.000	0.000	0.002
valid_cds	0.000	0.000	0.002
valid_tx	0.004	0.000	0.002