Package: miRNApath

Version: 1.44.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings miRNApath_1.44.0.tar.gz

StartedAt: 2019-10-16 03:14:06 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:15:05 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 59.0 seconds

RetCode: 0

Status:  OK

CheckDir: miRNApath.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings miRNApath_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/miRNApath.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRNApath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRNApath’ version ‘1.44.0’
* 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 ‘miRNApath’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘miRNApath’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  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
loadmirnapath: no visible global function definition for ‘read.table’
loadmirnapath: no visible global function definition for ‘new’
loadmirnapathways: no visible global function definition for
  ‘read.table’
loadmirnatogene: no visible global function definition for ‘read.table’
mirnaTable: no visible global function definition for ‘reshape’
runEnrichment :  : : no visible global function
  definition for ‘phyper’
runEnrichment: no visible global function definition for ‘slotNames’
Undefined global functions or variables:
  new phyper read.table reshape slotNames
Consider adding
  importFrom("methods", "new", "slotNames")
  importFrom("stats", "phyper", "reshape")
  importFrom("utils", "read.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mirnaTable 35.163   0.04  35.266
* 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-3.9-bioc/meat/miRNApath.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL miRNApath
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘miRNApath’ ...
** using staged installation
** R
** data
** 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 (miRNApath)

name	user	system	elapsed
checkColumns	0	0	0
convertFoldChange	0	0	0
filtermirnapath	0.052	0.000	0.051
loadmirnapath	0.079	0.004	0.083
loadmirnapathways	0.086	0.004	0.091
loadmirnatogene	0.183	0.004	0.187
miRNApath-package	0	0	0
mirnaTable	35.163	0.040	35.266
mirnaobj	0.033	0.000	0.034
mirnapath-class	0.023	0.000	0.023
runEnrichment	0	0	0