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CHECK report for DeconRNASeq on merida1

This page was generated on 2019-04-16 11:56:33 -0400 (Tue, 16 Apr 2019).

Package 379/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeconRNASeq 1.24.0
Ting Gong
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DeconRNASeq
Branch: RELEASE_3_8
Last Commit: 590bd50
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DeconRNASeq
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2019-04-15 23:23:57 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:24:46 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 49.6 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DeconRNASeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* 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
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 ‘plot’
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 plot prep pushViewport rainbow t.test title viewport
  xlab ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "plot", "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-3.8-bioc/meat/DeconRNASeq.Rcheck/00check.log’
for details.



Installation output

DeconRNASeq.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeconRNASeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DeconRNASeq’ ...
** 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
* DONE (DeconRNASeq)

Tests output


Example timings

DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings

nameusersystemelapsed
DeconRNASeq000
all.datasets0.0900.0100.101
array.proportions0.0640.0060.072
array.signatures0.0640.0060.070
condplot0.0640.0060.070
datasets0.1390.0110.152
fraction0.3990.0150.473
liver_kidney0.1340.0040.155
multi_tissue0.3830.0090.408
multiplot0.0040.0010.004
proportions0.1300.0040.136
signatures0.1380.0040.147
x.data0.3860.0090.399
x.signature0.3840.0100.405
x.signature.filtered0.3860.0110.442
x.signature.filtered.optimal0.3620.0090.399