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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 2026/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.60.0  (landing page)
Florence Cavalli
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/SpeCond
git_branch: RELEASE_3_20
git_last_commit: f57de9b
git_last_commit_date: 2024-10-29 09:32:51 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SpeCond on kjohnson1

To the developers/maintainers of the SpeCond package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpeCond.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpeCond
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpeCond.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpeCond_1.60.0.tar.gz
StartedAt: 2024-12-21 10:26:44 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 10:28:08 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 84.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpeCond.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpeCond_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpeCond.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpeCond/DESCRIPTION’ ... OK
* this is package ‘SpeCond’ version ‘1.60.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SpeCond’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘fields’ ‘hwriter’ ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
  fit1, param.detection = param.detection, multitest.correction.method
  = "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
  argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
  specificOutlierStep1 = specificOutlierStep1, param.detection =
  param.detection, multitest.correction.method =
  multitest.correction.method, prefix.file = prefix.file, print.hist.pv
  = print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nc' to 'ncol'
SpeCond: no visible global function definition for ‘is’
SpeCond: no visible global function definition for ‘new’
callMclustInStep2: no visible global function definition for ‘Mclust’
callMclustInStep2: no visible global function definition for
  ‘priorControl’
createSingleGeneHtmlPage: no visible global function definition for
  ‘openPage’
createSingleGeneHtmlPage: no visible global function definition for
  ‘hwrite’
createSingleGeneHtmlPage: no visible global function definition for
  ‘sessionInfo’
createSingleGeneHtmlPage: no visible global function definition for
  ‘closePage’
fitNoPriorWithExclusion : <anonymous>: no visible global function
  definition for ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
  ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
  ‘priorControl’
getDifferenceMedian: no visible global function definition for ‘median’
getExpressionpatternLegend: no visible global function definition for
  ‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘openPage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘is’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘png’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘barplot’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘dev.off’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘par’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘axis’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘points’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘legend’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘mtext’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘hwriteImage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘colorRampPalette’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘sessionInfo’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘closePage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘write.table’
getGeneHtmlPage: no visible global function definition for ‘is’
getGeneHtmlPage: no visible global function definition for ‘openPage’
getGeneHtmlPage: no visible global function definition for ‘hwrite’
getGeneHtmlPage: no visible global function definition for
  ‘sessionInfo’
getGeneHtmlPage: no visible global function definition for ‘closePage’
getHeatmap: no visible global function definition for ‘png’
getHeatmap: no visible global function definition for ‘heatmap’
getHeatmap: no visible global function definition for ‘colorbar.plot’
getHeatmap: no visible global function definition for ‘dev.off’
getHeatmap: no visible global function definition for ‘pdf’
getMatrixFromExpressionSet: no visible global function definition for
  ‘is’
getMatrixFromExpressionSet: no visible global function definition for
  ‘exprs’
getMinLoglikelihoodNull: no visible global function definition for
  ‘dnorm’
getPValueMean : <anonymous>: no visible global function definition for
  ‘pnorm’
getProfileHeatmap: no visible global function definition for ‘png’
getProfileHeatmap: no visible global function definition for ‘heatmap’
getProfileHeatmap: no visible global function definition for ‘dev.off’
getProfileHeatmap: no visible global function definition for ‘pdf’
getScaleMAD: no visible global function definition for ‘mad’
getSpecific: no visible global function definition for ‘pdf’
getSpecific: no visible global function definition for ‘hist’
getSpecific: no visible global function definition for ‘dev.off’
getSpecific: no visible global function definition for ‘p.adjust’
getSpecific: no visible global function definition for ‘new’
plotNormalMixture: no visible global function definition for ‘png’
plotNormalMixture: no visible global function definition for ‘points’
plotNormalMixture: no visible global function definition for
  ‘hwriteImage’
plotNormalMixture: no visible global function definition for ‘dev.off’
plotNormalMixture: no visible global function definition for ‘hist’
plotNormalMixture : f1: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f2: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f3: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f4: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f5: no visible global function definition for
  ‘dnorm’
plotNormalMixture: no visible global function definition for ‘lines’
plotNormalMixture: no visible global function definition for ‘legend’
plotNormalMixture : f_null : <anonymous>: no visible global function
  definition for ‘dnorm’
show.sp_list: no visible global function definition for ‘is’
writeGeneResult: no visible global function definition for
  ‘write.table’
writeSpeCondResult: no visible global function definition for
  ‘write.table’
writeUniqueProfileSpecificResult: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  Mclust axis barplot closePage colorRampPalette colorbar.plot dev.off
  dnorm exprs heatmap hist hwrite hwriteImage is legend lines mad
  median mtext new openPage p.adjust par pdf png pnorm points
  priorControl sessionInfo write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png")
  importFrom("graphics", "axis", "barplot", "hist", "legend", "lines",
             "mtext", "par", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm", "heatmap", "mad", "median", "p.adjust",
             "pnorm")
  importFrom("utils", "sessionInfo", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) getFullHtmlSpeCondResult.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) getProfile.Rd:12: Escaped LaTeX specials: \$ \$ \$
* 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 ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpeCond.Rcheck/00check.log’
for details.


Installation output

SpeCond.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpeCond
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SpeCond’ ...
** using staged installation
** R
** data
** 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 (SpeCond)

Tests output


Example timings

SpeCond.Rcheck/SpeCond-Ex.timings

nameusersystemelapsed
SpeCond3.1660.0273.210
createParameterMatrix0.0010.0010.001
expSetSpeCondExample0.0030.0030.006
expressionSpeCondExample0.0010.0020.004
fitNoPriorWithExclusion2.7770.0232.894
fitPrior1.5090.0121.628
getDefaultParameter0.0010.0000.000
getFullHtmlSpeCondResult4.3170.2634.768
getGeneHtmlPage4.0210.1974.254
getMatrixFromExpressionSet0.1290.0040.133
getProfile3.2830.0213.316
getSpecificOutliersStep12.0630.0112.080
getSpecificResult3.4210.0183.487
simulatedSpeCondData0.0030.0030.006
writeGeneResult3.5250.0213.578
writeSpeCondResult3.3900.0213.430
writeUniqueProfileSpecificResult3.0540.0193.095