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BioC 3.4: CHECK report for frmaTools on malbec1

This page was generated on 2017-04-15 16:10:00 -0400 (Sat, 15 Apr 2017).

Package 457/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frmaTools 1.26.0
Matthew N. McCall
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/frmaTools
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: frmaTools
Version: 1.26.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings frmaTools_1.26.0.tar.gz
StartedAt: 2017-04-14 22:36:33 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:37:22 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 48.5 seconds
RetCode: 0
Status:  OK 
CheckDir: frmaTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings frmaTools_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/frmaTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.26.0’
* 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 6.748  0.084   6.879
* 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-3.4-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
convertPlatform6.7480.0846.879
makeVectorPackage0.0000.0000.001