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This page was generated on 2021-10-15 15:06:33 -0400 (Fri, 15 Oct 2021).

CHECK results for DeconRNASeq on machv2

To the developers/maintainers of the DeconRNASeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeconRNASeq.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 458/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeconRNASeq 1.34.0  (landing page)
Ting Gong
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/DeconRNASeq
git_branch: RELEASE_3_13
git_last_commit: 69e542f
git_last_commit_date: 2021-05-19 11:53:59 -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: DeconRNASeq
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeconRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeconRNASeq_1.34.0.tar.gz
StartedAt: 2021-10-14 18:09:43 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:10:44 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DeconRNASeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeconRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeconRNASeq_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DeconRNASeq.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 ‘DeconRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeconRNASeq’ version ‘1.34.0’
* 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:
  .BBSoptions
  .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 ‘DeconRNASeq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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 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
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘grid’ ‘pcaMethods’
  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
DeconRNASeq: no visible global function definition for ‘prep’
DeconRNASeq: no visible global function definition for ‘pca’
DeconRNASeq: no visible global function definition for ‘R2cum’
DeconRNASeq: no visible global function definition for ‘ggplot’
DeconRNASeq: no visible global function definition for ‘aes’
DeconRNASeq: no visible global function definition for ‘geom_point’
DeconRNASeq: no visible global function definition for ‘labs’
DeconRNASeq: no visible global function definition for ‘geom_abline’
DeconRNASeq: no visible global function definition for ‘xlab’
DeconRNASeq: no visible global function definition for ‘ylab’
condplot: no visible global function definition for ‘rainbow’
condplot: no visible global function definition for ‘lines’
condplot: no visible global function definition for ‘axis’
condplot: no visible global function definition for ‘title’
decon.bootstrap: no visible global function definition for ‘t.test’
multiplot: no visible global function definition for ‘grid.newpage’
multiplot: no visible global function definition for ‘pushViewport’
multiplot: no visible global function definition for ‘viewport’
multiplot: no visible global function definition for ‘grid.layout’
multiplot : vplayout: no visible global function definition for
  ‘viewport’
Undefined global functions or variables:
  R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage
  labs lines pca prep pushViewport rainbow t.test title viewport xlab
  ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "title")
  importFrom("stats", "t.test")
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 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/DeconRNASeq.Rcheck/00check.log’
for details.



Installation output

DeconRNASeq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeconRNASeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘DeconRNASeq’ ...
** using staged installation
** R
** data
** demo
** 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 (DeconRNASeq)

Tests output


Example timings

DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings

nameusersystemelapsed
DeconRNASeq0.0010.0000.001
all.datasets0.0820.0090.091
array.proportions0.0550.0040.059
array.signatures0.0610.0050.066
condplot0.0610.0050.066
datasets0.1180.0060.124
fraction0.3570.0110.368
liver_kidney0.1190.0040.123
multi_tissue0.2760.0060.284
multiplot0.0010.0000.002
proportions0.1190.0040.123
signatures0.1300.0050.135
x.data0.3310.0100.343
x.signature0.2560.0060.262
x.signature.filtered0.3200.0070.327
x.signature.filtered.optimal0.3260.0080.335