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BioC 3.5: CHECK report for TargetScore on tokay2

This page was generated on 2017-10-18 14:22:44 -0400 (Wed, 18 Oct 2017).

Package 1303/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetScore 1.14.0
Yue Li
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/TargetScore
Branch: RELEASE_3_5
Last Commit: 0841319
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TargetScore
Version: 1.14.0
Command: rm -rf TargetScore.buildbin-libdir TargetScore.Rcheck && mkdir TargetScore.buildbin-libdir TargetScore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.14.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.14.0.tar.gz
StartedAt: 2017-10-18 03:22:10 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:23:40 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 89.8 seconds
RetCode: 0
Status:  OK  
CheckDir: TargetScore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TargetScore.buildbin-libdir TargetScore.Rcheck && mkdir TargetScore.buildbin-libdir TargetScore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.14.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/TargetScore.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetScore' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/TargetScore.Rcheck/00check.log'
for details.


TargetScore.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'TargetScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetScore' as TargetScore_1.14.0.zip
* DONE (TargetScore)

TargetScore.Rcheck/examples_i386/TargetScore-Ex.timings:

nameusersystemelapsed
TargetScore-package000
bsxfun.se000
dot.ext000
getTargetScores0.020.000.01
initialization0.040.000.05
logmvgamma000
logsumexp000
sort_components0.30.00.3
targetScore0.830.000.83
vbgmm0.100.000.09
vbound0.090.000.10
vexp0.090.000.09
vmax0.090.000.09

TargetScore.Rcheck/examples_x64/TargetScore-Ex.timings:

nameusersystemelapsed
TargetScore-package000
bsxfun.se000
dot.ext000
getTargetScores000
initialization0.030.000.03
logmvgamma0.010.000.01
logsumexp000
sort_components0.350.000.35
targetScore0.890.000.89
vbgmm0.110.000.11
vbound0.110.000.11
vexp0.090.000.09
vmax0.110.000.11