splicegear 1.48.0
Laurent Gautier
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/splicegear | | Branch: RELEASE_3_5 | | Last Commit: c60c698 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings splicegear_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/splicegear.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splicegear/DESCRIPTION’ ... OK
* this is package ‘splicegear’ version ‘1.48.0’
* 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 loading without being on the library search path ... 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 installed files from ‘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
‘/home/biocbuild/bbs-3.5-bioc/meat/splicegear.Rcheck/00check.log’
for details.