Package: GSEAlm

Version: 1.44.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEAlm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSEAlm_1.44.0.tar.gz

StartedAt: 2019-10-16 04:17:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:18:19 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 65.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSEAlm.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEAlm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSEAlm_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GSEAlm.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSEAlm/DESCRIPTION' ... OK
* this is package 'GSEAlm' version '1.44.0'
* 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 'GSEAlm' 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
* 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 ... NOTE
Package in Depends field not imported from: 'Biobase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pvalFromPermMat: warning in matrix(as.double(NA), nr = nrow(perms),
  ncol = 2): partial argument match of 'nr' to 'nrow'
CooksDPerGene: no visible global function definition for 'exprs'
dfbetasPerGene: no visible global function definition for 'exprs'
dfbetasPerGene: no visible global function definition for
  'featureNames'
dfbetasPerGene: no visible global function definition for 'sampleNames'
dffitsPerGene: no visible global function definition for 'exprs'
dffitsPerGene: no visible global function definition for 'featureNames'
dffitsPerGene : : no visible global function definition for
  'exprs'
getResidPerGene: no visible global function definition for 'exprs'
getResidPerGene: no visible global function definition for 'new'
getResidPerGene: no visible global function definition for 'phenoData'
gsealmPerm: no visible global function definition for 'pData'
gsealmPerm: no visible global function definition for 'pData<-'
lmPerGene: no visible global function definition for 'varLabels'
lmPerGene: no visible global function definition for 'pData'
lmPerGene: no visible global function definition for 'model.matrix'
lmPerGene: no visible global function definition for 'exprs'
mnDiffPlot: no visible global function definition for 'layout'
mnDiffPlot: no visible binding for global variable 'var'
mnDiffPlot: no visible global function definition for 'plot'
mnDiffPlot: no visible global function definition for 'abline'
mnDiffPlot: no visible global function definition for 'lines'
mnDiffPlot: no visible global function definition for 'predict'
mnDiffPlot: no visible global function definition for 'loess'
resplot: no visible global function definition for 'layout'
resplot: no visible global function definition for 'boxplot'
resplot: no visible global function definition for 'lines'
restrip: no visible global function definition for 'layout'
restrip: no visible global function definition for 'stripchart'
restrip: no visible global function definition for 'title'
restrip: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline boxplot exprs featureNames layout lines loess model.matrix new
  pData pData<- phenoData plot predict sampleNames stripchart title var
  varLabels
Consider adding
  importFrom("graphics", "abline", "boxplot", "layout", "lines", "plot",
             "stripchart", "title")
  importFrom("methods", "new")
  importFrom("stats", "loess", "model.matrix", "predict", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: gsealmPerm.Rd:62: Dropping empty section \references
* 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 files in 'vignettes' ... NOTE
The following files contain a license that requires
distribution of original sources:
  'crop.sty'
Please ensure that you have complied with it.
* 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-3.9-bioc/meat/GSEAlm.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GSEAlm_1.44.0.tar.gz && rm -rf GSEAlm.buildbin-libdir && mkdir GSEAlm.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSEAlm.buildbin-libdir GSEAlm_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GSEAlm_1.44.0.zip && rm GSEAlm_1.44.0.tar.gz GSEAlm_1.44.0.zip
###
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install for i386

* installing *source* package 'GSEAlm' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSEAlm'
    finding HTML links ... done
    GSNormalize                             html  
    dfbetasPerGene                          html  
    getResidPerGene                         html  
    gsealmPerm                              html  
    lmPerGene                               html  
    resplot                                 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 'GSEAlm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEAlm' as GSEAlm_1.44.0.zip
* DONE (GSEAlm)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GSEAlm' successfully unpacked and MD5 sums checked