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CHECK report for TargetScore on veracruz1

This page was generated on 2018-04-12 13:37:07 -0400 (Thu, 12 Apr 2018).

Package 1383/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetScore 1.16.0
Yue Li
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/TargetScore
Branch: RELEASE_3_6
Last Commit: db90bab
Last Changed Date: 2017-10-30 12:40:04 -0400 (Mon, 30 Oct 2017)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TargetScore
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TargetScore_1.16.0.tar.gz
StartedAt: 2018-04-12 10:10:45 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:11:38 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TargetScore.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TargetScore_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TargetScore.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/TargetScore.Rcheck/00check.log’
for details.



Installation output

TargetScore.Rcheck/00install.out

* 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)

Tests output


Example timings

TargetScore.Rcheck/TargetScore-Ex.timings

nameusersystemelapsed
TargetScore-package0.0010.0000.001
bsxfun.se0.0010.0000.001
dot.ext0.0010.0010.001
getTargetScores0.0050.0000.005
initialization0.0370.0030.039
logmvgamma0.0020.0000.002
logsumexp0.0010.0000.001
sort_components0.4560.0070.473
targetScore0.6140.0080.637
vbgmm0.0860.0010.092
vbound0.1010.0000.101
vexp0.0970.0010.098
vmax0.0950.0000.095