Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-14 12:05:45 -0400 (Thu, 14 Oct 2021).

CHECK results for PROPER on riesling1

To the developers/maintainers of the PROPER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PROPER.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1450/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PROPER 1.25.0  (landing page)
Hao Wu
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/PROPER
git_branch: master
git_last_commit: 16895ad
git_last_commit_date: 2021-05-19 12:10:06 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: PROPER
Version: 1.25.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PROPER_1.25.0.tar.gz
StartedAt: 2021-10-14 02:41:23 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 02:44:57 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PROPER.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PROPER_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/PROPER.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.25.0'
* 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 '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' call not declared from: 'edgeR'
'library' or 'require' calls in package code:
  '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.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 '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 estimateTagwiseDisp estimateTrendedDisp exactTest
  exprs grid hist legend matplot median mtext newSeqCountSet p.adjust
  par results rgamma rnorm rpois sd text topTags waldTest
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "grid",
             "hist", "legend", "matplot", "mtext", "par", "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 (user + system) or elapsed time > 5s
         user system elapsed
runSims 17.25   0.23   17.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
runSims 15.92   0.09   16.02
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/PROPER.Rcheck/00check.log'
for details.



Installation output

PROPER.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PROPER_1.25.0.tar.gz && rm -rf PROPER.buildbin-libdir && mkdir PROPER.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PROPER.buildbin-libdir PROPER_1.25.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PROPER_1.25.0.zip && rm PROPER_1.25.0.tar.gz PROPER_1.25.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1596k  100 1596k    0     0  4666k      0 --:--:-- --:--:-- --:--:-- 4666k

install for i386

* installing *source* package 'PROPER' ...
** using staged installation
** 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 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 'PROPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PROPER' as PROPER_1.25.0.zip
* DONE (PROPER)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'PROPER' successfully unpacked and MD5 sums checked

Tests output


Example timings

PROPER.Rcheck/examples_i386/PROPER-Ex.timings

nameusersystemelapsed
RNAseq.SimOptions.2grp0.30.00.3
comparePower000
estParam000
plotPowerHist000
plots000
power.seqDepth000
runSims17.25 0.2317.49
simRNAseq0.190.020.20
summaryPower000

PROPER.Rcheck/examples_x64/PROPER-Ex.timings

nameusersystemelapsed
RNAseq.SimOptions.2grp0.230.020.25
comparePower000
estParam000
plotPowerHist000
plots000
power.seqDepth000
runSims15.92 0.0916.02
simRNAseq0.170.000.17
summaryPower000