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This page was generated on 2021-10-15 15:06:39 -0400 (Fri, 15 Oct 2021).

CHECK results for HTqPCR on machv2

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.

raw results

Package 876/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTqPCR 1.46.0  (landing page)
Heidi Dvinge
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/HTqPCR
git_branch: RELEASE_3_13
git_last_commit: 3c75acb
git_last_commit_date: 2021-05-19 11:44:16 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HTqPCR
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HTqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HTqPCR_1.46.0.tar.gz
StartedAt: 2021-10-14 20:03:43 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:04:59 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 75.5 seconds
RetCode: 0
Status:   OK  
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HTqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HTqPCR_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/HTqPCR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTqPCR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTqPCR’ version ‘1.46.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 sizes of PDF files under ‘inst/doc’ ... 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/HTqPCR.Rcheck/00check.log’
for details.



Installation output

HTqPCR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HTqPCR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘HTqPCR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output


Example timings

HTqPCR.Rcheck/HTqPCR-Ex.timings

nameusersystemelapsed
changeCtLayout0.2640.0070.270
clusterCt0.1100.0140.124
filterCategory0.0920.0070.098
filterCtData0.5080.0050.513
limmaCtData0.0840.0070.090
normalizeCtData0.6550.0410.703
plotCVBoxes0.1570.0080.166
plotCtArray0.1050.0060.112
plotCtBoxes0.0470.0060.053
plotCtCard0.1500.0130.163
plotCtCategory0.7490.0090.759
plotCtCor0.0680.0040.072
plotCtDensity0.0260.0030.029
plotCtHeatmap1.7390.0331.774
plotCtHistogram0.0160.0040.019
plotCtOverview0.0680.0060.074
plotCtPCA0.0260.0030.030
plotCtPairs0.6380.0260.665
plotCtReps0.2450.0090.257
plotCtScatter0.1420.0090.152
plotCtVariation0.4030.0220.426
plotGenes0.0190.0050.065
qPCRpros0.0040.0010.005
qPCRraw0.0040.0010.005
qPCRset-class0.0600.0070.066
readCtData0.0700.0040.075
setCategory0.0460.0030.048