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CHECK report for splicegear on merida1

This page was generated on 2019-04-16 11:54:01 -0400 (Tue, 16 Apr 2019).

Package 1492/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splicegear 1.54.0
Laurent Gautier
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/splicegear
Branch: RELEASE_3_8
Last Commit: 6b897ff
Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: splicegear
Version: 1.54.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splicegear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splicegear_1.54.0.tar.gz
StartedAt: 2019-04-16 02:56:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:58:27 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:  OK 
CheckDir: splicegear.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splicegear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splicegear_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/splicegear.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 ‘splicegear/DESCRIPTION’ ... OK
* this is package ‘splicegear’ version ‘1.54.0’
* 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 ‘splicegear’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘methods’
A package should be listed in only one of these fields.
* 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

buildSpliceSites: warning in matrix(unlist(spsiteIpos[spsiteIpos.i]),
  nc = 2, byrow = TRUE): partial argument match of 'nc' to 'ncol'
getRelSignStrength: warning in matrix(NaN, nc = ncol(x), nr = nrow(x)):
  partial argument match of 'nr' to 'nrow'
getRelSignStrength: warning in matrix(NaN, nc = ncol(x), nr = nrow(x)):
  partial argument match of 'nc' to 'ncol'
grid.plot.Probes: warning in viewport(xscale = xlim, yscale = ylim, w =
  0.9, h = 0.9): partial argument match of 'w' to 'width'
grid.plot.Probes: warning in viewport(xscale = xlim, yscale = ylim, w =
  0.9, h = 0.9): partial argument match of 'h' to 'height'
grid.plot.SpliceSites: warning in viewport(xscale = xlim, yscale =
  ylim, w = 0.9, h = 0.9): partial argument match of 'w' to 'width'
grid.plot.SpliceSites: warning in viewport(xscale = xlim, yscale =
  ylim, w = 0.9, h = 0.9): partial argument match of 'h' to 'height'
plot.SpliceExprSet: warning in layout(matrix(c(1, 2), 1, 2), width =
  fig.xratio, height = fig.yratio): partial argument match of 'width'
  to 'widths'
plot.SpliceExprSet: warning in layout(matrix(c(1, 2), 1, 2), width =
  fig.xratio, height = fig.yratio): partial argument match of 'height'
  to 'heights'
* checking Rd files ... NOTE
prepare_Rd: isProbeOnSpliceSite.Rd:18-19: Dropping empty section \details
prepare_Rd: isProbeOnSpliceSite.Rd:31-33: Dropping empty section \examples
prepare_Rd: sort.SpliceExprSet.Rd:18-20: Dropping empty section \details
prepare_Rd: spliceset.Rd:29-31: Dropping empty section \source
* 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
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/splicegear.Rcheck/00check.log’
for details.



Installation output

splicegear.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL splicegear
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘splicegear’ ...
** R
** data
** 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 (splicegear)

Tests output


Example timings

splicegear.Rcheck/splicegear-Ex.timings

nameusersystemelapsed
Probes-class0.0320.0080.039
SpliceExprSet-class0.0570.0060.065
SpliceSites-class0.0720.0070.079
SpliceSitesGenomic-class0.0090.0010.010
as.data.frame.SpliceExprSet0.0640.0080.074
barplot.SpliceSites0.0100.0020.013
buildSpliceSites0.2880.0180.312
getRelSignStrength0.0580.0040.064
grid.plot.SpliceSites0.1860.0030.191
plot.SpliceExprSet0.0450.0030.048
plot.SpliceSites0.0080.0020.009
plot.SpliceSitesGenomic0.0060.0010.007
sort.SpliceExprSet0.0030.0010.005
spliceset0.0220.0010.024
split.SpliceSites0.0030.0020.004