Package: SPLINTER

Version: 1.9.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SPLINTER_1.9.1.tar.gz

StartedAt: 2019-04-09 03:50:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:55:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 299.7 seconds

RetCode: 0

Status:  OK

CheckDir: SPLINTER.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SPLINTER_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SPLINTER.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
eventPlot            10.738  0.192  11.107
addEnsemblAnnotation  0.493  0.044  12.515
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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	0.003	0.000	0.003
addEnsemblAnnotation	0.493	0.044	12.515
callPrimer3	0	0	0
checkPrimer	0.111	0.000	0.111
compatible_cds	0.002	0.000	0.002
compatible_tx	0.001	0.000	0.002
donor.m	0.001	0.000	0.002
eventOutcomeCompare	2.428	0.020	2.473
eventOutcomeTranslate	0.455	0.023	0.498
eventPlot	10.738	0.192	11.107
extendROI	0.766	0.000	0.767
extractSpliceEvents	0.004	0.000	0.004
extractSpliceSites	0.086	0.000	0.085
findCompatibleEvents	0.335	0.003	0.339
findCompatibleExon	0.21	0.00	0.21
findTX	0.007	0.000	0.006
getPCRsizes	3.368	0.135	4.476
getRegionDNA	0.219	0.000	0.218
insertRegion	0.118	0.000	0.119
makeROI	0.238	0.000	0.239
makeUniqueIDs	0.003	0.000	0.003
pcr_result1	0.001	0.000	0.000
plot_seqlogo	0.040	0.000	0.039
primers	0.000	0.000	0.001
psiPlot	0.201	0.004	0.205
region_minus_exon	0.001	0.000	0.001
roi	0.000	0.000	0.001
shapiroAcceptor	0.381	0.000	0.415
shapiroDonor	0.346	0.004	0.350
splice_data	0.001	0.000	0.001
splice_fasta	0.000	0.000	0.001
splitPCRhit	0	0	0
thecds	0.000	0.001	0.000
theexons	0.000	0.000	0.001
valid_cds	0.001	0.000	0.001
valid_tx	0.001	0.000	0.001