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BioC 3.5: CHECK report for HTqPCR on tokay2

This page was generated on 2017-08-16 13:20:23 -0400 (Wed, 16 Aug 2017).

Package 636/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTqPCR 1.30.0
Heidi Dvinge
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/HTqPCR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HTqPCR
Version: 1.30.0
Command: rm -rf HTqPCR.buildbin-libdir HTqPCR.Rcheck && mkdir HTqPCR.buildbin-libdir HTqPCR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.30.0.tar.gz >HTqPCR.Rcheck\00install.out 2>&1 && cp HTqPCR.Rcheck\00install.out HTqPCR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.30.0.tar.gz
StartedAt: 2017-08-16 00:31:44 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:33:34 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 110.3 seconds
RetCode: 0
Status:  OK  
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HTqPCR.buildbin-libdir HTqPCR.Rcheck && mkdir HTqPCR.buildbin-libdir HTqPCR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.30.0.tar.gz >HTqPCR.Rcheck\00install.out 2>&1 && cp HTqPCR.Rcheck\00install.out HTqPCR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/HTqPCR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTqPCR' version '1.30.0'
* 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 'HTqPCR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'limma' 'RColorBrewer'
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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmapSig: warning in heatmap.2(data, trace = "none", density.info =
  "none", col = col, distfun = d, breaks = b, mar = mar, ...): partial
  argument match of 'mar' to 'margins'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'n' to 'number'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'sort' to 'sort.by'
plotCtCor: warning in heatmap.2(x, col = col, breaks = b, scale =
  "none", dendrogram = "row", trace = "none", main = main, density.info
  = "none", mar = mar, ...): partial argument match of 'mar' to
  'margins'
plotCtHeatmap: warning in heatmap.2(data, trace = "none", density.info
  = "none", main = main, col = col, distfun = d, breaks = breaks, mar =
  mar, ...): partial argument match of 'mar' to 'margins'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra = 0.001):
  partial argument match of 'sfra' to 'sfrac'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD.ratio[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra =
  0.001): partial argument match of 'sfra' to 'sfrac'
.readCtBioMark: no visible global function definition for 'read.csv'
.readCtCFX: no visible global function definition for 'read.csv'
.readCtOpenArray: no visible global function definition for 'read.csv'
cbind.qPCRset: no visible global function definition for 'phenoData<-'
cbind.qPCRset: no visible global function definition for
  'AnnotatedDataFrame'
cbind.qPCRset: no visible global function definition for 'pData'
cbind.qPCRset: no visible global function definition for
  'capture.output'
changeCtLayout: no visible global function definition for
  'featureData<-'
changeCtLayout: no visible global function definition for 'featureData'
changeCtLayout: no visible global function definition for 'phenoData<-'
changeCtLayout: no visible global function definition for
  'capture.output'
filterCategory: no visible global function definition for
  'capture.output'
filterCtData: no visible binding for global variable 'IQR'
filterCtData: no visible global function definition for
  'capture.output'
mannwhitneyCtData : <anonymous>: no visible global function definition
  for 'wilcox.test'
normalizeCtData: no visible global function definition for
  'capture.output'
rbind.qPCRset: no visible global function definition for
  'featureData<-'
rbind.qPCRset: no visible global function definition for
  'AnnotatedDataFrame'
rbind.qPCRset: no visible global function definition for 'fData'
rbind.qPCRset: no visible global function definition for
  'capture.output'
readCtData: no visible global function definition for
  'AnnotatedDataFrame'
readCtData: no visible global function definition for 'capture.output'
setCategory: no visible global function definition for 'capture.output'
[,qPCRset: no visible global function definition for 'phenoData<-'
[,qPCRset: no visible global function definition for 'phenoData'
exprs,qPCRset: no visible global function definition for
  'assayDataElement'
exprs<-,qPCRset-ANY: no visible global function definition for
  'assayDataElementReplace'
featureCategory,qPCRset: no visible global function definition for
  'assayDataElement'
featureCategory<-,qPCRset: no visible global function definition for
  'assayDataElementReplace'
featureClass,qPCRset: no visible global function definition for 'fData'
featureClass<-,qPCRset: no visible global function definition for
  'fData'
featureClass<-,qPCRset: no visible global function definition for
  'fData<-'
featureNames,qPCRset: no visible global function definition for 'fData'
featureNames<-,qPCRset-character: no visible global function definition
  for 'fData'
featureNames<-,qPCRset-character: no visible global function definition
  for 'fData<-'
featurePos,qPCRset: no visible global function definition for 'fData'
featurePos<-,qPCRset: no visible global function definition for 'fData'
featurePos<-,qPCRset: no visible global function definition for
  'fData<-'
featureType,qPCRset: no visible global function definition for 'fData'
featureType<-,qPCRset: no visible global function definition for
  'fData'
featureType<-,qPCRset: no visible global function definition for
  'fData<-'
flag,qPCRset: no visible global function definition for
  'assayDataElement'
flag<-,qPCRset: no visible global function definition for
  'assayDataElementReplace'
Undefined global functions or variables:
  AnnotatedDataFrame IQR assayDataElement assayDataElementReplace
  capture.output fData fData<- featureData featureData<- pData
  phenoData phenoData<- read.csv wilcox.test
Consider adding
  importFrom("stats", "IQR", "wilcox.test")
  importFrom("utils", "capture.output", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: cbind.Rd:35-36: Dropping empty section \examples
prepare_Rd: heatmapSig.Rd:31-32: Dropping empty section \examples
prepare_Rd: mannwhitneyCtData.Rd:52-62: Dropping empty section \examples
prepare_Rd: plotCtRQ.Rd:46-48: Dropping empty section \examples
prepare_Rd: plotCtSignificance.Rd:46-47: Dropping empty section \examples
prepare_Rd: ttestCtData.Rd:49-50: Dropping empty section \examples
* 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 ...
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/HTqPCR.Rcheck/00check.log'
for details.


HTqPCR.Rcheck/00install.out:


install for i386

* installing *source* package 'HTqPCR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'HTqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HTqPCR' as HTqPCR_1.30.0.zip
* DONE (HTqPCR)

HTqPCR.Rcheck/examples_i386/HTqPCR-Ex.timings:

nameusersystemelapsed
changeCtLayout0.300.010.31
clusterCt0.770.050.82
filterCategory0.090.000.10
filterCtData0.470.020.48
limmaCtData0.250.000.25
normalizeCtData0.430.010.44
plotCVBoxes0.120.000.12
plotCtArray0.140.000.15
plotCtBoxes0.050.020.06
plotCtCard0.120.000.12
plotCtCategory0.420.000.42
plotCtCor0.910.000.91
plotCtDensity0.080.001.06
plotCtHeatmap1.340.051.39
plotCtHistogram0.020.010.03
plotCtOverview0.220.000.22
plotCtPCA0.060.000.07
plotCtPairs0.340.020.35
plotCtReps0.10.00.1
plotCtScatter0.040.000.05
plotCtVariation0.300.010.31
plotGenes0.050.000.04
qPCRpros000
qPCRraw0.010.000.02
qPCRset-class0.080.000.08
readCtData0.170.000.17
setCategory0.100.000.09

HTqPCR.Rcheck/examples_x64/HTqPCR-Ex.timings:

nameusersystemelapsed
changeCtLayout0.420.020.44
clusterCt0.780.010.80
filterCategory0.060.000.06
filterCtData0.390.000.39
limmaCtData0.250.000.25
normalizeCtData0.470.030.50
plotCVBoxes0.170.000.17
plotCtArray0.190.000.19
plotCtBoxes0.110.000.11
plotCtCard0.190.020.20
plotCtCategory0.670.030.71
plotCtCor0.940.000.93
plotCtDensity0.030.000.04
plotCtHeatmap2.240.002.24
plotCtHistogram0.030.000.03
plotCtOverview0.330.020.34
plotCtPCA0.100.000.09
plotCtPairs0.500.010.52
plotCtReps0.140.000.14
plotCtScatter0.090.020.11
plotCtVariation0.600.010.60
plotGenes0.040.020.07
qPCRpros0.000.010.01
qPCRraw0.020.000.02
qPCRset-class0.110.000.11
readCtData0.220.000.22
setCategory0.120.020.14