Package: splicegear

Version: 1.56.0

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_1.56.0.tar.gz

StartedAt: 2019-10-16 07:05:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:08:06 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 134.3 seconds

RetCode: 0

Status:  OK

CheckDir: splicegear.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.56.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/splicegear.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.56.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.SpliceExprSet as.data.frame.SpliceSites
  barplot.SpliceSites plot.Probes plot.SpliceExprSet plot.SpliceSites
  plot.SpliceSitesGenomic sort.SpliceExprSet split.SpliceSites
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/splicegear.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL splicegear
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘splicegear’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (splicegear)

name	user	system	elapsed
Probes-class	0.033	0.009	0.041
SpliceExprSet-class	0.068	0.004	0.072
SpliceSites-class	0.087	0.007	0.094
SpliceSitesGenomic-class	0.010	0.001	0.048
as.data.frame.SpliceExprSet	0.068	0.008	0.077
barplot.SpliceSites	0.009	0.003	0.013
buildSpliceSites	0.640	0.023	0.664
getRelSignStrength	0.088	0.024	0.112
grid.plot.SpliceSites	0.358	0.070	0.428
plot.SpliceExprSet	0.057	0.006	0.063
plot.SpliceSites	0.011	0.005	0.018
plot.SpliceSitesGenomic	0.008	0.002	0.010
sort.SpliceExprSet	0.004	0.003	0.007
spliceset	0.030	0.001	0.033
split.SpliceSites	0.003	0.003	0.006