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CHECK report for frma on merida1

This page was generated on 2019-04-16 11:55:09 -0400 (Tue, 16 Apr 2019).

Package 560/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frma 1.34.0
Matthew N. McCall
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/frma
Branch: RELEASE_3_8
Last Commit: 2d39fc6
Last Changed Date: 2018-10-30 11:41:46 -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: frma
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:frma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings frma_1.34.0.tar.gz
StartedAt: 2019-04-16 00:01:05 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:04:51 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 226.8 seconds
RetCode: 0
Status:  OK 
CheckDir: frma.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:frma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings frma_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/frma.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 ‘frma/DESCRIPTION’ ... OK
* this is package ‘frma’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘frma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
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
GNUSE: no visible binding for global variable ‘median’
GNUSE: no visible binding for global variable ‘quantile’
GNUSE: no visible global function definition for ‘boxplot’
barcode: no visible global function definition for ‘pnorm’
batchFit: no visible global function definition for ‘median’
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for ‘slot<-’
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for ‘slot’
randomeffects<-,frmaExpressionSet: no visible global function
  definition for ‘validObject’
residuals<-,frmaExpressionSet: no visible global function definition
  for ‘validObject’
se.exprs<-,ExpressionSet: no visible global function definition for
  ‘validObject’
se.exprs<-,frmaExpressionSet: no visible global function definition for
  ‘validObject’
weights<-,frmaExpressionSet: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
GNUSE   17.567  3.260  21.023
frma    11.120  2.933  14.133
barcode 11.021  2.911  14.023
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/frma.Rcheck/00check.log’
for details.



Installation output

frma.Rcheck/00install.out

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

Tests output


Example timings

frma.Rcheck/frma-Ex.timings

nameusersystemelapsed
GNUSE17.567 3.26021.023
barcode11.021 2.91114.023
frma11.120 2.93314.133
frmaExpressionSet-class0.1020.0000.102