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BioC 3.5: CHECK report for frmaTools on malbec2

This page was generated on 2017-08-16 13:13:29 -0400 (Wed, 16 Aug 2017).

Package 482/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frmaTools 1.28.0
Matthew N. McCall
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/frmaTools
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: frmaTools
Version: 1.28.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings frmaTools_1.28.0.tar.gz
StartedAt: 2017-08-15 23:07:52 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:08:44 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 51.7 seconds
RetCode: 0
Status:  OK 
CheckDir: frmaTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings frmaTools_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/frmaTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘frmaTools/DESCRIPTION’ ... OK
* this is package ‘frmaTools’ version ‘1.28.0’
* 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:
  inst/VectorPkg-template/data/.dummy.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 ‘frmaTools’ 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 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 ‘oligo’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘affy’
  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
convertPlatform: no visible global function definition for
  ‘cleancdfname’
convertPlatform: no visible global function definition for ‘cdfName’
convertPlatform: no visible global function definition for ‘probeNames’
convertPlatform: no visible global function definition for ‘pmindex’
getFidMetaProbesetCore: no visible global function definition for ‘db’
getFidMetaProbesetExtended: no visible global function definition for
  ‘db’
getFidMetaProbesetFull: no visible global function definition for ‘db’
getFidProbeset: no visible global function definition for ‘db’
makeMaps: no visible global function definition for ‘xy2indices’
makeVectorsAffyBatch: no visible global function definition for
  ‘ReadAffy’
makeVectorsAffyBatch: no visible global function definition for
  ‘bg.correct.rma’
makeVectorsAffyBatch: no visible global function definition for ‘pm’
makeVectorsAffyBatch: no visible global function definition for
  ‘probeNames’
makeVectorsAffyBatch: no visible global function definition for
  ‘pmindex’
makeVectorsAffyBatch: no visible global function definition for
  ‘packageVersion’
makeVectorsFeatureSet: no visible global function definition for
  ‘read.celfiles’
makeVectorsFeatureSet: no visible global function definition for
  ‘backgroundCorrect’
Undefined global functions or variables:
  ReadAffy backgroundCorrect bg.correct.rma cdfName cleancdfname db
  packageVersion pm pmindex probeNames read.celfiles xy2indices
Consider adding
  importFrom("utils", "packageVersion")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
convertPlatform 8.464  0.128   9.467
* 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-3.5-bioc/meat/frmaTools.Rcheck/00check.log’
for details.


frmaTools.Rcheck/00install.out:

* installing *source* package ‘frmaTools’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (frmaTools)

frmaTools.Rcheck/frmaTools-Ex.timings:

nameusersystemelapsed
convertPlatform8.4640.1289.467
makeVectorPackage000