arrayQuality 1.15.0
Agnes Paquet
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/arrayQuality | | Last Changed Rev: 27716 / Revision: 29143 | | Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/arrayQuality.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.15.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayQuality' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... WARNING
Found the following file(s) with non-portable file names:
inst/doc/meeboQuality guide.htm
inst/doc/meeboQuality guide_files
These are not fully portable file names
See section 'Package structure' in manual 'Writing R Extensions'.
* 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 name space can be loaded with stated dependencies ... 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
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'
PRvQCHyb: no visible binding for global variable 'MmDEGenes'
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'
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'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating arrayQuality-Ex.R ... OK
* checking examples ... OK
* creating arrayQuality-manual.tex ... OK
* checking arrayQuality-manual.tex ... OK
WARNING: There was 1 warning, see
D:/biocbld/bbs-2.2-bioc/meat/arrayQuality.Rcheck/00check.log
for details
installing R.css in D:/biocbld/bbs-2.2-bioc/meat/arrayQuality.Rcheck
---------- Making package arrayQuality ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing inst files
installing data files
preparing package arrayQuality for lazy loading
Loading required package: marray
Loading required package: limma
Loading required package: convert
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: hexbin
Loading required package: grid
Loading required package: lattice
Loading required package: gridBase
Loading required package: RColorBrewer
Warning in namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: summary
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'PRv9mers' on or after line 36
Note: unmatched right brace in 'PRv9mers.Rd' on or after line 36
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: unmatched right brace in 'scaleRefTable' on or after line 11
Note: unmatched right brace in 'scaleRefTable' on or after line 32
Note: unmatched right brace in 'scaleRefTable.Rd' on or after line 11
Note: unmatched right brace in 'scaleRefTable.Rd' on or after line 32
Note: removing empty section \examples
Note: removing empty section \examples
>>> Building/Updating help pages for package 'arrayQuality'
Formats: text html latex example chm
MmDEGenes text html latex chm
PRv9mers text html latex example chm
PRvQCHyb text html latex example chm
agQuality text html latex example chm
arrayQuality-internal text html latex chm
globalQuality text html latex example chm
gpQuality text html latex example chm
gprDB text html latex chm
heeboQuality text html latex example chm
heeboQualityPlots text html latex example chm
maQualityPlots text html latex example chm
meeboQuality text html latex example chm
meeboQualityPlots text html latex example chm
prdata text html latex chm
qualBoxplot text html latex example chm
qualityScore text html latex chm
readAgilent text html latex chm
readGPR text html latex example chm
readSpikeTypes text html latex example chm
readSpot text html latex chm
readcontrolCode text html latex chm
scaleRefTable text html latex chm
slideQuality text html latex example chm
spotQuality text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.2-bioc\meat\arrayQuality.Rcheck\00_pkg_src\arrayQuality\chm\arrayQuality.chm
Compile time: 0 minutes, 0 seconds
25 Topics
137 Local links
0 Internet links
1 Graphic
Created d:\biocbld\bbs-2.2-bioc\meat\arrayQuality.Rcheck\00_pkg_src\arrayQuality\chm\arrayQuality.chm, 45,043 bytes
Compression decreased file by 61,221 bytes.
adding MD5 sums
* DONE (arrayQuality)