Heidi Dvinge
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/HTqPCR |
| git_branch: master |
| git_last_commit: 4bf8b27 |
| git_last_commit_date: 2021-10-26 11:54:57 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:46 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the HTqPCR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTqPCR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 890/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HTqPCR 1.49.0 (landing page) Heidi Dvinge
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: HTqPCR |
| Version: 1.49.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HTqPCR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HTqPCR_1.49.0.tar.gz |
| StartedAt: 2022-03-17 19:20:07 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:21:04 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 57.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HTqPCR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HTqPCR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HTqPCR_1.49.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/HTqPCR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.49.0'
* 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
* 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'
.readCtBioMark: no visible global function definition for 'read.csv'
.readCtCFX: no visible global function definition for 'read.csv'
.readCtOpenArray: no visible global function definition for 'read.csv'
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'
cbind.qPCRset: no visible global function definition for
'capture.output'
changeCtLayout: no visible global function definition for
'featureData<-'
changeCtLayout: no visible global function definition for 'featureData'
changeCtLayout: no visible global function definition for 'phenoData<-'
changeCtLayout: no visible global function definition for
'capture.output'
filterCategory: no visible global function definition for
'capture.output'
filterCtData: no visible binding for global variable 'IQR'
filterCtData: no visible global function definition for
'capture.output'
mannwhitneyCtData : <anonymous>: no visible global function definition
for 'wilcox.test'
normalizeCtData: no visible global function definition for
'capture.output'
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'
rbind.qPCRset: no visible global function definition for
'capture.output'
readCtData: no visible global function definition for
'AnnotatedDataFrame'
readCtData: no visible global function definition for 'capture.output'
setCategory: no visible global function definition for 'capture.output'
[,qPCRset: no visible global function definition for 'phenoData<-'
[,qPCRset: 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: no visible global function definition for
'assayDataElementReplace'
featureClass,qPCRset: no visible global function definition for 'fData'
featureClass<-,qPCRset: no visible global function definition for
'fData'
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'
featurePos<-,qPCRset: 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'
featureType<-,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'
flag<-,qPCRset: no visible global function definition for
'assayDataElementReplace'
Undefined global functions or variables:
AnnotatedDataFrame IQR assayDataElement assayDataElementReplace
capture.output fData fData<- featureData featureData<- pData
phenoData phenoData<- read.csv wilcox.test
Consider adding
importFrom("stats", "IQR", "wilcox.test")
importFrom("utils", "capture.output", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: cbind.Rd:35-36: Dropping empty section \examples
prepare_Rd: heatmapSig.Rd:31-32: Dropping empty section \examples
prepare_Rd: mannwhitneyCtData.Rd:52-62: Dropping empty section \examples
prepare_Rd: plotCtRQ.Rd:46-48: Dropping empty section \examples
prepare_Rd: plotCtSignificance.Rd:46-47: Dropping empty section \examples
prepare_Rd: ttestCtData.Rd:49-50: 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 files in 'vignettes' ... OK
* checking examples ... 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/HTqPCR.Rcheck/00check.log'
for details.
HTqPCR.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL HTqPCR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'HTqPCR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HTqPCR'
finding HTML links ... done
HTqPCR-package html
cbind html
changeCtLayout html
clusterCt html
filterCategory html
filterCtData html
heatmapSig html
limmaCtData html
mannwhitneyCtData html
normalizeCtData html
plotCVBoxes html
plotCtArray html
plotCtBoxes html
plotCtCard html
plotCtCategory html
plotCtCor html
plotCtDensity html
plotCtHeatmap html
plotCtHistogram html
plotCtOverview html
plotCtPCA html
plotCtPairs html
plotCtRQ html
plotCtReps html
plotCtScatter html
plotCtSignificance html
plotCtVariation html
plotGenes html
qPCRpros html
qPCRraw html
qPCRset-class html
finding level-2 HTML links ... done
readCtData html
setCategory html
ttestCtData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTqPCR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'logitT' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'STATegRa' is missing or broken
done
HTqPCR.Rcheck/HTqPCR-Ex.timings
| name | user | system | elapsed | |
| changeCtLayout | 0.12 | 0.00 | 0.12 | |
| clusterCt | 0.08 | 0.00 | 0.08 | |
| filterCategory | 0.03 | 0.00 | 0.03 | |
| filterCtData | 0.19 | 0.01 | 0.20 | |
| limmaCtData | 0.03 | 0.02 | 0.05 | |
| normalizeCtData | 0.55 | 0.00 | 0.55 | |
| plotCVBoxes | 0.11 | 0.00 | 0.11 | |
| plotCtArray | 0.04 | 0.02 | 0.06 | |
| plotCtBoxes | 0.03 | 0.00 | 0.03 | |
| plotCtCard | 0.08 | 0.00 | 0.08 | |
| plotCtCategory | 0.32 | 0.03 | 0.34 | |
| plotCtCor | 0.06 | 0.00 | 0.06 | |
| plotCtDensity | 0.01 | 0.00 | 0.02 | |
| plotCtHeatmap | 0.68 | 0.01 | 0.69 | |
| plotCtHistogram | 0 | 0 | 0 | |
| plotCtOverview | 0.03 | 0.00 | 0.03 | |
| plotCtPCA | 0.03 | 0.00 | 0.04 | |
| plotCtPairs | 0.57 | 0.00 | 0.56 | |
| plotCtReps | 0.17 | 0.00 | 0.17 | |
| plotCtScatter | 0.03 | 0.02 | 0.05 | |
| plotCtVariation | 0.30 | 0.00 | 0.29 | |
| plotGenes | 0.01 | 0.01 | 0.04 | |
| qPCRpros | 0 | 0 | 0 | |
| qPCRraw | 0.02 | 0.00 | 0.01 | |
| qPCRset-class | 0.04 | 0.00 | 0.05 | |
| readCtData | 0.02 | 0.04 | 0.04 | |
| setCategory | 0.00 | 0.01 | 0.02 | |