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BioC 3.4: CHECK report for TargetScore on tokay1

This page was generated on 2017-04-15 16:18:02 -0400 (Sat, 15 Apr 2017).

Package 1225/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetScore 1.12.0
Yue Li
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TargetScore
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TargetScore
Version: 1.12.0
Command: rm -rf TargetScore.buildbin-libdir TargetScore.Rcheck && mkdir TargetScore.buildbin-libdir TargetScore.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.12.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.12.0.tar.gz
StartedAt: 2017-04-15 01:08:22 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:09:32 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 69.4 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.12.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/TargetScore.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.12.0'
* 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 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-3.4-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_1.12.0.zip
* DONE (TargetScore)

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

nameusersystemelapsed
TargetScore-package000
bsxfun.se000
dot.ext000
getTargetScores000
initialization0.010.000.01
logmvgamma000
logsumexp000
sort_components0.170.020.19
targetScore0.720.010.74
vbgmm0.100.000.09
vbound0.090.000.09
vexp0.090.000.09
vmax0.090.000.10

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

nameusersystemelapsed
TargetScore-package000
bsxfun.se000
dot.ext000
getTargetScores0.010.000.02
initialization000
logmvgamma000
logsumexp000
sort_components0.250.010.26
targetScore1.220.001.22
vbgmm0.120.000.12
vbound0.130.000.13
vexp0.140.000.14
vmax0.120.000.13