Package: splicegear

Version: 1.58.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:splicegear.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings splicegear_1.58.0.tar.gz

StartedAt: 2020-04-15 06:50:45 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:52:49 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 124.5 seconds

RetCode: 0

Status:  OK

CheckDir: splicegear.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:splicegear.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings splicegear_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/splicegear.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'splicegear/DESCRIPTION' ... OK
* this is package 'splicegear' version '1.58.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/splicegear.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/splicegear_1.58.0.tar.gz && rm -rf splicegear.buildbin-libdir && mkdir splicegear.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=splicegear.buildbin-libdir splicegear_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL splicegear_1.58.0.zip && rm splicegear_1.58.0.tar.gz splicegear_1.58.0.zip
###
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install for i386

* installing *source* package 'splicegear' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'splicegear'
    finding HTML links ... done
    Probes-class                            html  
    SpliceExprSet-class                     html  
    SpliceSites-class                       html  
    SpliceSitesGenomic-class                html  
    as.data.frame.SpliceExprSet             html  
    barplot.SpliceSites                     html  
    buildSpliceSites                        html  
    getRelSignStrength                      html  
    grid.helpers                            html  
    grid.plot.SpliceSites                   html  
    isProbeOnSpliceSite                     html  
    matchprobes2Probes                      html  
    plot.SpliceExprSet                      html  
    plot.SpliceSites                        html  
    plot.SpliceSitesGenomic                 html  
    sort.SpliceExprSet                      html  
    spliceset                               html  
    split.SpliceSites                       html  
** 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

install for x64

* installing *source* package 'splicegear' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'splicegear' as splicegear_1.58.0.zip
* DONE (splicegear)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'splicegear' successfully unpacked and MD5 sums checked