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BioC 2.13: CHECK report for HTqPCR on moscato1

This page was generated on 2014-04-05 09:49:58 -0700 (Sat, 05 Apr 2014).

Package 350/750HostnameOS / ArchBUILDCHECKBUILD BIN
HTqPCR 1.16.0
Heidi Dvinge
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/HTqPCR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: HTqPCR
Version: 1.16.0
Command: rm -rf HTqPCR.buildbin-libdir && mkdir HTqPCR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.16.0.tar.gz >HTqPCR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.16.0.tar.gz && mv HTqPCR.buildbin-libdir/* HTqPCR.Rcheck/ && rmdir HTqPCR.buildbin-libdir
StartedAt: 2014-04-05 04:35:35 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:38:02 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 147.1 seconds
RetCode: 0
Status:  OK  
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/HTqPCR.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.16.0'
* 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'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'HTqPCR.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
setCategory 5.11   0.08    5.23
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
setCategory 6.61   0.04    6.66
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-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_1.16.0.zip
* DONE (HTqPCR)

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

nameusersystemelapsed
HTqPCR-package2.950.053.00
cbind0.080.000.07
changeCtLayout0.140.000.14
clusterCt0.190.000.19
filterCategory0.060.010.08
filterCtData0.260.000.26
heatmapSig1.020.001.02
limmaCtData0.560.000.56
mannwhitneyCtData0.960.000.96
normalizeCtData0.450.000.45
plotCVBoxes0.150.000.15
plotCtArray0.160.000.16
plotCtBoxes0.040.000.05
plotCtCard0.060.000.06
plotCtCategory2.200.022.22
plotCtCor0.050.000.05
plotCtDensity0.050.010.06
plotCtHeatmap1.730.001.73
plotCtHistogram0.030.000.03
plotCtOverview0.110.000.11
plotCtPCA0.040.000.05
plotCtPairs0.570.000.56
plotCtRQ0.280.000.28
plotCtReps0.130.000.13
plotCtScatter0.030.000.03
plotCtSignificance0.390.000.39
plotCtVariation0.540.000.55
plotGenes0.050.000.04
qPCRpros000
qPCRraw0.000.020.02
qPCRset-class0.080.000.08
readCtData0.140.000.14
setCategory5.110.085.23
ttestCtData0.750.010.76

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

nameusersystemelapsed
HTqPCR-package3.850.043.88
cbind0.100.000.09
changeCtLayout0.190.000.19
clusterCt0.270.000.27
filterCategory0.070.000.07
filterCtData0.220.000.22
heatmapSig1.110.011.13
limmaCtData0.570.020.58
mannwhitneyCtData1.090.001.09
normalizeCtData0.470.010.48
plotCVBoxes0.170.020.19
plotCtArray0.150.000.16
plotCtBoxes0.070.000.06
plotCtCard0.070.000.08
plotCtCategory2.970.002.96
plotCtCor0.040.000.05
plotCtDensity0.050.000.04
plotCtHeatmap2.260.002.27
plotCtHistogram0.030.000.34
plotCtOverview0.180.010.19
plotCtPCA0.040.000.04
plotCtPairs0.880.000.88
plotCtRQ0.520.000.52
plotCtReps0.180.020.22
plotCtScatter0.070.000.06
plotCtSignificance0.560.000.56
plotCtVariation0.560.000.64
plotGenes0.030.000.03
qPCRpros0.020.000.02
qPCRraw0.030.000.03
qPCRset-class0.060.010.08
readCtData0.160.000.15
setCategory6.610.046.66
ttestCtData1.450.001.45