Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:04:48 -0500 (Fri, 26 Nov 2021).

CHECK results for ConsensusClusterPlus on nebbiolo2

To the developers/maintainers of the ConsensusClusterPlus package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ConsensusClusterPlus.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 386/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ConsensusClusterPlus 1.58.0  (landing page)
Matt Wilkerson
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/ConsensusClusterPlus
git_branch: RELEASE_3_14
git_last_commit: d8131dd
git_last_commit_date: 2021-10-26 11:55:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: ConsensusClusterPlus
Version: 1.58.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ConsensusClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ConsensusClusterPlus_1.58.0.tar.gz
StartedAt: 2021-11-25 08:55:47 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 08:56:12 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 25.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ConsensusClusterPlus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ConsensusClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ConsensusClusterPlus_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ConsensusClusterPlus.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ConsensusClusterPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ConsensusClusterPlus’ version ‘1.58.0’
* 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 ‘ConsensusClusterPlus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  GPL version 2
Standardizable: TRUE
Standardized license specification:
  GPL-2
* 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 ... NOTE
Namespace in Imports field not imported from: ‘ALL’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
  = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
  labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
  sep = ""), ColSideCol = oc): partial argument match of 'mar' to
  'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
  = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
  labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
  sep = ""), ColSideCol = oc): partial argument match of 'ColSideCol'
  to 'ColSideColors'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
  Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
  labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
  k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
  match of 'mar' to 'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
  Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
  labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
  k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
  match of 'ColSideCol' to 'ColSideColors'
ConsensusClusterPlus: no visible global function definition for
  ‘bitmap’
ConsensusClusterPlus: no visible global function definition for
  ‘postscript’
calcICL: no visible global function definition for ‘postscript’
calcICL: no visible global function definition for ‘bitmap’
Undefined global functions or variables:
  bitmap postscript
Consider adding
  importFrom("grDevices", "bitmap", "postscript")
to your NAMESPACE file.
* 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 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ConsensusClusterPlus.Rcheck/00check.log’
for details.



Installation output

ConsensusClusterPlus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ConsensusClusterPlus
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ConsensusClusterPlus’ ...
** using staged installation
** R
** 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 (ConsensusClusterPlus)

Tests output


Example timings

ConsensusClusterPlus.Rcheck/ConsensusClusterPlus-Ex.timings

nameusersystemelapsed
ConsensusClusterPlus1.1570.0851.241