BioC 3.4: CHECK report for TargetScore on malbec1

Package: TargetScore

Version: 1.12.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TargetScore_1.12.0.tar.gz

StartedAt: 2017-04-15 01:35:43 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:36:22 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 38.3 seconds

RetCode: 0

Status:  OK

CheckDir: TargetScore.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TargetScore_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TargetScore.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 ‘TargetScore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetScore’ version ‘1.12.0’
* 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 ‘TargetScore’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dot.ext: no visible global function definition for ‘size’
getTargetScores: no visible global function definition for
  ‘get_TargetScanHuman_contextScore’
getTargetScores: no visible global function definition for
  ‘get_TargetScanHuman_PCT’
getTargetScores: no visible global function definition for
  ‘get_validated_targets’
getTargetScores: no visible global function definition for
  ‘get_miRNA_family_info’
getTargetScores: no visible binding for global variable ‘logFC.imputed’
getTargetScores : <anonymous>: no visible global function definition
  for ‘cor’
getTargetScores: no visible global function definition for ‘aggregate’
logmvgamma: no visible global function definition for ‘size’
targetScore: no visible global function definition for ‘as.roman’
targetScore : <anonymous>: no visible global function definition for
  ‘as.roman’
targetScore: no visible global function definition for ‘sigmoid’
Undefined global functions or variables:
  aggregate as.roman cor get_TargetScanHuman_PCT
  get_TargetScanHuman_contextScore get_miRNA_family_info
  get_validated_targets logFC.imputed sigmoid size
Consider adding
  importFrom("stats", "aggregate", "cor")
  importFrom("utils", "as.roman")
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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/TargetScore.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
TargetScore-package	0	0	0
bsxfun.se	0.000	0.000	0.001
dot.ext	0.000	0.000	0.001
getTargetScores	0.004	0.000	0.002
initialization	0.012	0.000	0.011
logmvgamma	0.000	0.000	0.001
logsumexp	0.000	0.000	0.001
sort_components	0.216	0.012	0.229
targetScore	0.792	0.000	0.795
vbgmm	0.108	0.000	0.107
vbound	0.108	0.000	0.109
vexp	0.108	0.000	0.106
vmax	0.104	0.000	0.104