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BioC 3.0: CHECK report for HTqPCR on moscato1

This page was generated on 2015-04-10 09:46:01 -0700 (Fri, 10 Apr 2015).

Package 432/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTqPCR 1.20.0
Heidi Dvinge
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/HTqPCR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: HTqPCR
Version: 1.20.0
Command: rm -rf HTqPCR.buildbin-libdir HTqPCR.Rcheck && mkdir HTqPCR.buildbin-libdir HTqPCR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.20.0.tar.gz >HTqPCR.Rcheck\00install.out 2>&1 && cp HTqPCR.Rcheck\00install.out HTqPCR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.20.0.tar.gz
StartedAt: 2015-04-10 02:14:30 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:16:50 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 139.8 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.20.0.tar.gz >HTqPCR.Rcheck\00install.out 2>&1 && cp HTqPCR.Rcheck\00install.out HTqPCR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/HTqPCR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.20.0'
* 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'
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'
changeCtLayout: no visible global function definition for
  'featureData<-'
changeCtLayout: no visible global function definition for 'featureData'
changeCtLayout: no visible global function definition for 'phenoData<-'
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'
readCtData: no visible global function definition for
  'AnnotatedDataFrame'
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'
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'
featureType,qPCRset: no visible global function definition for 'fData'
flag,qPCRset: no visible global function definition for
  'assayDataElement'
* checking Rd files ... OK
* 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' ... [23s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
setCategory 5.89   0.14    6.67
** running examples for arch 'x64' ... [21s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
setCategory 4.07   0.06    5.29
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.20.0.zip
* DONE (HTqPCR)

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

nameusersystemelapsed
HTqPCR-package2.220.012.23
cbind0.120.000.12
changeCtLayout0.10.00.1
clusterCt0.230.020.25
filterCategory0.060.000.06
filterCtData0.160.000.16
heatmapSig1.010.011.34
limmaCtData0.450.000.45
mannwhitneyCtData0.960.000.95
normalizeCtData0.390.020.41
plotCVBoxes0.140.000.14
plotCtArray0.140.000.14
plotCtBoxes0.050.000.05
plotCtCard0.030.020.05
plotCtCategory0.560.010.58
plotCtCor0.030.020.05
plotCtDensity0.060.000.06
plotCtHeatmap1.720.001.72
plotCtHistogram0.030.000.03
plotCtOverview0.090.000.09
plotCtPCA0.050.000.05
plotCtPairs0.760.041.07
plotCtRQ0.440.020.46
plotCtReps0.170.000.17
plotCtScatter0.030.000.03
plotCtSignificance0.560.000.57
plotCtVariation0.830.000.92
plotGenes0.030.000.03
qPCRpros000
qPCRraw0.000.020.02
qPCRset-class0.110.000.11
readCtData0.220.000.22
setCategory5.890.146.67
ttestCtData1.130.001.13

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

nameusersystemelapsed
HTqPCR-package2.610.002.60
cbind0.140.000.14
changeCtLayout0.100.000.09
clusterCt0.250.000.25
filterCategory0.070.000.06
filterCtData0.170.000.17
heatmapSig1.050.011.06
limmaCtData0.540.000.65
mannwhitneyCtData1.10.01.1
normalizeCtData0.370.020.39
plotCVBoxes0.140.010.15
plotCtArray0.160.000.16
plotCtBoxes0.040.000.05
plotCtCard0.070.000.06
plotCtCategory0.650.000.65
plotCtCor0.050.000.05
plotCtDensity0.040.000.05
plotCtHeatmap2.050.002.13
plotCtHistogram0.010.000.02
plotCtOverview0.130.000.12
plotCtPCA0.050.000.05
plotCtPairs0.590.020.63
plotCtRQ0.450.000.45
plotCtReps0.110.000.11
plotCtScatter0.030.000.03
plotCtSignificance0.370.000.38
plotCtVariation0.470.030.50
plotGenes0.010.020.03
qPCRpros000
qPCRraw000
qPCRset-class0.060.000.07
readCtData0.130.010.14
setCategory4.070.065.29
ttestCtData0.860.000.85