Multiple platform build/check report for BioC 3.9 - CHECK report for SPLINTER on celaya2

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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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SPLINTER.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.1’
* 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 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            12.859  0.705  13.570
getPCRsizes           5.115  0.376   5.500
addEnsemblAnnotation  0.456  0.057  17.248
* 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

Installation output

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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/3.6/Resources/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)

Tests output

Example timings

name	user	system	elapsed
acceptor.m	0.002	0.001	0.003
addEnsemblAnnotation	0.456	0.057	17.248
callPrimer3	0.001	0.000	0.001
checkPrimer	0.152	0.023	0.175
compatible_cds	0.002	0.002	0.004
compatible_tx	0.002	0.002	0.004
donor.m	0.002	0.002	0.004
eventOutcomeCompare	2.986	0.088	3.077
eventOutcomeTranslate	0.577	0.016	0.594
eventPlot	12.859	0.705	13.570
extendROI	0.853	0.056	0.908
extractSpliceEvents	0.004	0.000	0.004
extractSpliceSites	0.159	0.031	0.190
findCompatibleEvents	0.360	0.001	0.361
findCompatibleExon	0.217	0.002	0.218
findTX	0.010	0.001	0.009
getPCRsizes	5.115	0.376	5.500
getRegionDNA	0.482	0.013	0.494
insertRegion	0.166	0.002	0.169
makeROI	0.360	0.003	0.362
makeUniqueIDs	0.007	0.001	0.007
pcr_result1	0.001	0.001	0.002
plot_seqlogo	0.055	0.001	0.056
primers	0.002	0.002	0.004
psiPlot	0.435	0.005	0.440
region_minus_exon	0.001	0.002	0.004
roi	0.002	0.002	0.004
shapiroAcceptor	0.761	0.024	0.788
shapiroDonor	0.772	0.030	0.803
splice_data	0.002	0.002	0.004
splice_fasta	0.002	0.002	0.004
splitPCRhit	0.001	0.000	0.002
thecds	0.002	0.001	0.003
theexons	0.002	0.001	0.004
valid_cds	0.003	0.002	0.004
valid_tx	0.002	0.002	0.004

CHECK report for SPLINTER on celaya2

Summary

Command output

Installation output

Tests output

Example timings