Package: SPLINTER

Version: 1.12.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SPLINTER_1.12.0.tar.gz

StartedAt: 2020-04-15 04:13:03 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:18:57 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 354.1 seconds

RetCode: 0

Status:  OK

CheckDir: SPLINTER.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SPLINTER_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SPLINTER.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getPCRsizes 16.696  0.200  18.069
eventPlot   13.440  0.096  13.605
* 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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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SPLINTER
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SPLINTER’ ...
** using staged installation
** 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 from temporary location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package can be loaded from final location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package keeps a record of temporary installation path
* DONE (SPLINTER)

name	user	system	elapsed
acceptor.m	0.004	0.000	0.003
addEnsemblAnnotation	1.672	0.000	3.966
callPrimer3	0	0	0
checkPrimer	0.108	0.000	0.107
compatible_cds	0.000	0.000	0.001
compatible_tx	0	0	0
donor.m	0	0	0
eventOutcomeCompare	2.036	0.168	2.260
eventOutcomeTranslate	0.776	0.012	0.790
eventPlot	13.440	0.096	13.605
extendROI	1.44	0.00	1.44
extractSpliceEvents	0.004	0.000	0.005
extractSpliceSites	0.140	0.000	0.141
findCompatibleEvents	0.648	0.000	0.650
findCompatibleExon	0.392	0.000	0.396
findTX	0.032	0.000	0.038
getPCRsizes	16.696	0.200	18.069
getRegionDNA	0.292	0.000	0.292
insertRegion	0.192	0.004	0.197
makeROI	0.580	0.004	0.587
makeUniqueIDs	0.004	0.000	0.005
pcr_result1	0.004	0.000	0.001
plot_seqlogo	0.068	0.000	0.070
primers	0.000	0.000	0.001
psiPlot	0.392	0.008	0.406
region_minus_exon	0.000	0.000	0.001
roi	0.000	0.004	0.001
shapiroAcceptor	0.772	0.000	0.811
shapiroDonor	0.784	0.004	0.794
splice_data	0.004	0.000	0.001
splice_fasta	0	0	0
splitPCRhit	0.012	0.000	0.010
thecds	0	0	0
theexons	0.000	0.000	0.001
valid_cds	0.000	0.000	0.001
valid_tx	0	0	0