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Package 43/553HostnameOS / ArchBUILDCHECKBUILD BIN
arrayQuality 1.34.0
Agnes Paquet
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/arrayQuality
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: arrayQuality
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch arrayQuality_1.34.0.tar.gz
StartedAt: 2012-09-23 23:17:43 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:18:44 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 60.4 seconds
RetCode: 0
Status:  OK 
CheckDir: arrayQuality.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/arrayQuality.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.34.0'
* 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 whether package 'arrayQuality' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 44.7Mb
  sub-directories of 1Mb or more:
    Heebo      17.1Mb
    Meebo      12.2Mb
    gprQCData  14.9Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 for unstated 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
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
  6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
  argument match of 'width' to 'widths'
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
  6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
  argument match of 'height' to 'heights'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
  4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
  2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
  of 'width' to 'widths'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
  4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
  2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
  of 'height' to 'heights'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
  partial argument match of 'x' to 'xvar'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
  partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
heeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId,
  meeboAnnot = HEEBOset): partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
  colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
  HEEBOset): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
maQualityPlots: warning in qpDotPlots(mnorm, xvar = "maM", col =
  colcode, main = "Control normalized M", cex.main = 0.8, id =
  controlId): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in qpDotPlots(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId): partial
  argument match of 'col' to 'colcode'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
meeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId,
  meeboAnnot = MEEBOset): partial argument match of 'col' to 'colcode'
meeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
  colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
  MEEBOset): partial argument match of 'col' to 'colcode'
qpBEplot.linear: warning in axis(1, at = seq(-50, 120, 10), label =
  seq(50, -120, -10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = seq(0, 90, 10), label = seq(0,
  90, 10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = c(-10, 100), label = c("WT",
  "Neg ctl")): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(4, at =
  quantile(mnorm$A[coreCollection, 1], c(0.25, 0.75, 0.9, 1), na.rm =
  TRUE), label = c(0.25, 0.75, 0.9, 1), las = 2): partial argument
  match of 'label' to 'labels'
qpTiling: warning in axis(1, at = unique(sort(-as.numeric(distance))),
  label = rev(unique(sort(as.numeric(distance))))): partial argument
  match of 'label' to 'labels'
PRvQCHyb: no visible binding for global variable 'MmDEGenes'
Spike.Cy5vsCy3: no visible binding for global variable 'MEEBOset'
Spike.Cy5vsCy3: no visible binding for global variable 'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOset'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOctrl'
Spike.MM.Scatter: no visible binding for global variable 'RG'
Spike.MM.Scatter: no visible binding for global variable 'MEEBOset'
Spike.MMplot: no visible binding for global variable 'RG'
Spike.MMplot: no visible binding for global variable 'MEEBOset'
Spike.Sensitivity: no visible binding for global variable 'RG'
Spike.Sensitivity: no visible binding for global variable 'MEEBOset'
arrayScal: no visible binding for global variable 'MmReferenceDB'
getSpikeIds: no visible binding for global variable 'MEEBOset'
getSpikeIndex: no visible binding for global variable 'MEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOctrl'
heeboQuality: no visible binding for global variable 'HEEBOtilingres'
heeboQualityPlots: no visible binding for global variable 'HEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOctrl'
meeboQuality: no visible binding for global variable 'MEEBOtilingres'
meeboQualityPlots: no visible binding for global variable 'MEEBOset'
qpBEplot.linear: no visible binding for global variable 'MEEBOctrl'
qpBoxplotMeebo: no visible binding for global variable 'MEEBOset'
qpDotPlotsEEBO: no visible binding for global variable 'MEEBOset'
qpDotPlotsMeebo: no visible binding for global variable 'MEEBOset'
qpMisMatchPlot: no visible binding for global variable 'HEEBOctrl'
qpTiling: no visible binding for global variable 'MEEBOtilingres'
qualBoxplot: no visible binding for global variable 'MmReferenceDB'
qualBoxplot: no visible binding for global variable 'HsReferenceDB'
qualityScore: no visible binding for global variable 'MmReferenceDB'
readAllSpikes: no visible binding for global variable 'MEEBOset'
scaleRefTable: no visible binding for global variable 'MmReferenceDB'
* checking Rd files ... NOTE
prepare_Rd: spotQuality.Rd:92-93: 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' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/arrayQuality.Rcheck/00check.log'
for details.

arrayQuality.Rcheck/00install.out:

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

* DONE (arrayQuality)

arrayQuality.Rcheck/arrayQuality-Ex.timings:

nameusersystemelapsed
PRv9mers0.0030.0030.006
PRvQCHyb0.0030.0020.005
agQuality0.0030.0000.004
globalQuality0.0030.0030.005
gpQuality0.0030.0020.006
heeboQuality0.0000.0000.001
heeboQualityPlots0.0010.0000.001
maQualityPlots0.0000.0000.001
meeboQuality000
meeboQualityPlots0.0010.0010.001
qualBoxplot0.0030.0020.006
readGPR0.0030.0020.005
readSpikeTypes0.0030.0030.005
slideQuality0.0030.0020.006