HTqPCR 1.24.0
Heidi Dvinge
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/HTqPCR | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf HTqPCR.buildbin-libdir HTqPCR.Rcheck && mkdir HTqPCR.buildbin-libdir HTqPCR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTqPCR.buildbin-libdir HTqPCR_1.24.0.tar.gz >HTqPCR.Rcheck\00install.out 2>&1 && cp HTqPCR.Rcheck\00install.out HTqPCR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=HTqPCR.buildbin-libdir --install="check:HTqPCR-install.out" --force-multiarch --no-vignettes --timings HTqPCR_1.24.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/HTqPCR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.24.0'
* 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'
[,qPCRset : .local: no visible global function definition for
'featureData<-'
[,qPCRset : .local: no visible global function definition for
'featureData'
[,qPCRset : .local: no visible global function definition for
'phenoData<-'
[,qPCRset : .local: 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 : .local: no visible global function
definition for 'assayDataElementReplace'
featureClass,qPCRset: no visible global function definition for 'fData'
featureClass<-,qPCRset : .local: no visible global function definition
for 'fData'
featureClass<-,qPCRset : .local: 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 : .local: no visible global function definition
for 'fData'
featurePos<-,qPCRset : .local: no visible global function definition
for 'fData<-'
featureType,qPCRset: no visible global function definition for 'fData'
featureType<-,qPCRset : .local: no visible global function definition
for 'fData'
featureType<-,qPCRset : .local: no visible global function definition
for 'fData<-'
flag,qPCRset: no visible global function definition for
'assayDataElement'
flag<-,qPCRset : .local: no visible global function definition for
'assayDataElementReplace'
* 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 4.34 0.07 5.36
** running examples for arch 'x64' ... [24s] 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: 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/HTqPCR.Rcheck/00check.log'
for details.