Package: frmaTools

Version: 1.38.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings frmaTools_1.38.0.tar.gz

StartedAt: 2020-04-15 00:45:29 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:46:08 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 38.7 seconds

RetCode: 0

Status:  OK

CheckDir: frmaTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings frmaTools_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/frmaTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.38.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
convertPlatform 8.004  0.184   8.779
* 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-3.10-bioc/meat/frmaTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL frmaTools
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘frmaTools’ ...
** using staged installation
** 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 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 (frmaTools)

name	user	system	elapsed
convertPlatform	8.004	0.184	8.779
makeVectorPackage	0	0	0