Package: PROPER

Version: 1.14.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PROPER_1.14.1.tar.gz

StartedAt: 2019-04-13 04:41:32 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:43:50 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 137.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PROPER.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PROPER_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PROPER.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PROPER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PROPER' version '1.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'PROPER' 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 ... WARNING
'library' or 'require' calls not declared from:
  'DESeq2' 'edgeR'
'library' or 'require' calls in package code:
  'DESeq' 'DESeq2' 'DSS' 'edgeR'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'edgeR'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNAseq.SimOptions.2grp: no visible global function definition for
  'data'
RNAseq.SimOptions.2grp: no visible binding for global variable 'cheung'
add.axis1: no visible global function definition for 'axis'
add.axis1: no visible global function definition for 'text'
comparePower: no visible global function definition for 'p.adjust'
estParam: no visible global function definition for 'exprs'
getDisp1: no visible global function definition for 'median'
getDisp2: no visible global function definition for 'DGEList'
getDisp2: no visible global function definition for
  'estimateCommonDisp'
getDisp2: no visible global function definition for
  'estimateTrendedDisp'
getDisp2: no visible global function definition for
  'estimateTagwiseDisp'
lfc.alt: no visible global function definition for 'rnorm'
lfc.null: no visible global function definition for 'rnorm'
plotAll: no visible global function definition for 'par'
plotAll: no visible global function definition for 'mtext'
plotFDR: no visible global function definition for 'matplot'
plotFDR: no visible global function definition for 'mtext'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'box'
plotFDR: no visible global function definition for 'grid'
plotFDR: no visible global function definition for 'legend'
plotFDcost : <anonymous>: no visible global function definition for
  'sd'
plotFDcost: no visible global function definition for 'matplot'
plotFDcost: no visible global function definition for 'arrows'
plotFDcost: no visible global function definition for 'mtext'
plotFDcost: no visible global function definition for 'axis'
plotFDcost: no visible global function definition for 'box'
plotFDcost: no visible global function definition for 'grid'
plotFDcost: no visible global function definition for 'legend'
plotPower: no visible binding for global variable 'sd'
plotPower: no visible global function definition for 'matplot'
plotPower: no visible global function definition for 'arrows'
plotPower: no visible global function definition for 'mtext'
plotPower: no visible global function definition for 'legend'
plotPower: no visible global function definition for 'grid'
plotPower: no visible global function definition for 'axis'
plotPower: no visible global function definition for 'box'
plotPowerAlpha: no visible binding for global variable 'sd'
plotPowerAlpha: no visible global function definition for 'matplot'
plotPowerAlpha: no visible global function definition for 'arrows'
plotPowerAlpha: no visible global function definition for 'mtext'
plotPowerAlpha: no visible global function definition for 'axis'
plotPowerAlpha: no visible global function definition for 'box'
plotPowerAlpha: no visible global function definition for 'grid'
plotPowerAlpha: no visible global function definition for 'abline'
plotPowerAlpha: no visible global function definition for 'legend'
plotPowerFD: no visible binding for global variable 'sd'
plotPowerFD: no visible global function definition for 'matplot'
plotPowerFD: no visible global function definition for 'arrows'
plotPowerFD: no visible global function definition for 'mtext'
plotPowerFD: no visible global function definition for 'axis'
plotPowerFD: no visible global function definition for 'box'
plotPowerFD: no visible global function definition for 'grid'
plotPowerFD: no visible global function definition for 'legend'
plotPowerHist: no visible global function definition for 'axis'
plotPowerTD: no visible binding for global variable 'sd'
plotPowerTD: no visible global function definition for 'matplot'
plotPowerTD: no visible global function definition for 'arrows'
plotPowerTD: no visible global function definition for 'mtext'
plotPowerTD: no visible global function definition for 'axis'
plotPowerTD: no visible global function definition for 'box'
plotPowerTD: no visible global function definition for 'grid'
plotPowerTD: no visible global function definition for 'legend'
rnegbinom: no visible global function definition for 'rpois'
rnegbinom: no visible global function definition for 'rgamma'
run.DESeq: no visible global function definition for 'newCountDataSet'
run.DESeq: no visible global function definition for
  'estimateSizeFactors'
run.DESeq: no visible global function definition for
  'estimateDispersions'
run.DESeq: no visible global function definition for 'nbinomTest'
run.DESeq2: no visible global function definition for
  'DESeqDataSetFromMatrix'
run.DESeq2: no visible global function definition for 'DataFrame'
run.DESeq2: no visible global function definition for 'DESeq'
run.DESeq2: no visible global function definition for 'results'
run.DSS: no visible global function definition for 'newSeqCountSet'
run.DSS: no visible global function definition for 'estNormFactors'
run.DSS: no visible global function definition for 'estDispersion'
run.DSS: no visible global function definition for 'waldTest'
run.edgeR: no visible global function definition for 'DGEList'
run.edgeR: no visible global function definition for 'calcNormFactors'
run.edgeR: no visible global function definition for
  'estimateCommonDisp'
run.edgeR: no visible global function definition for
  'estimateTagwiseDisp'
run.edgeR: no visible global function definition for 'exactTest'
run.edgeR: no visible global function definition for 'topTags'
runSims: no visible global function definition for 'median'
setBaselineExpr.seqDepth: no visible global function definition for
  'data'
table2hist: no visible global function definition for 'hist'
table2hist: no visible global function definition for 'rnorm'
table2hist: no visible global function definition for 'plot'
table2hist: no visible global function definition for 'axis'
table2hist: no visible global function definition for 'box'
Undefined global functions or variables:
  DESeq DESeqDataSetFromMatrix DGEList DataFrame abline arrows axis box
  calcNormFactors cheung data estDispersion estNormFactors
  estimateCommonDisp estimateDispersions estimateSizeFactors
  estimateTagwiseDisp estimateTrendedDisp exactTest exprs grid hist
  legend matplot median mtext nbinomTest newCountDataSet newSeqCountSet
  p.adjust par plot results rgamma rnorm rpois sd text topTags waldTest
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "grid",
             "hist", "legend", "matplot", "mtext", "par", "plot", "text")
  importFrom("stats", "median", "p.adjust", "rgamma", "rnorm", "rpois",
             "sd")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
  Code: function(X, type = 1)
  Docs: function(X, type = c(1, 2))
  Mismatches in argument default values:
    Name: 'type' Code: 1 Docs: c(1, 2)

* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
runSims 25.38   0.17   25.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
runSims 23.38   0.22   23.64
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/PROPER.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/PROPER_1.14.1.tar.gz && rm -rf PROPER.buildbin-libdir && mkdir PROPER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PROPER.buildbin-libdir PROPER_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PROPER_1.14.1.zip && rm PROPER_1.14.1.tar.gz PROPER_1.14.1.zip
###
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install for i386

* installing *source* package 'PROPER' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PROPER'
    finding HTML links ... done
    RNAseq.SimOptions.2grp                  html  
    comparePower                            html  
    estParam                                html  
    historicalData                          html  
    plotPowerHist                           html  
    plots                                   html  
    power.seqDepth                          html  
    runSims                                 html  
    simRNAseq                               html  
    summaryPower                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PROPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PROPER' as PROPER_1.14.1.zip
* DONE (PROPER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PROPER' successfully unpacked and MD5 sums checked
In R CMD INSTALL