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BioC 3.5: CHECK report for Clomial on tokay2

This page was generated on 2017-10-18 14:23:15 -0400 (Wed, 18 Oct 2017).

Package 229/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clomial 1.12.0
Habil Zare
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Clomial
Branch: RELEASE_3_5
Last Commit: ded61ae
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: Clomial
Version: 1.12.0
Command: rm -rf Clomial.buildbin-libdir Clomial.Rcheck && mkdir Clomial.buildbin-libdir Clomial.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clomial.buildbin-libdir Clomial_1.12.0.tar.gz >Clomial.Rcheck\00install.out 2>&1 && cp Clomial.Rcheck\00install.out Clomial-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Clomial.buildbin-libdir --install="check:Clomial-install.out" --force-multiarch --no-vignettes --timings Clomial_1.12.0.tar.gz
StartedAt: 2017-10-17 22:47:10 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:52:49 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 339.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Clomial.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Clomial.buildbin-libdir Clomial.Rcheck && mkdir Clomial.buildbin-libdir Clomial.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clomial.buildbin-libdir Clomial_1.12.0.tar.gz >Clomial.Rcheck\00install.out 2>&1 && cp Clomial.Rcheck\00install.out Clomial-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Clomial.buildbin-libdir --install="check:Clomial-install.out" --force-multiarch --no-vignettes --timings Clomial_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Clomial.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 'Clomial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clomial' 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 'Clomial' 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
Clomial: no visible global function definition for 'runif'
Clomial.generate.data: no visible global function definition for
  'runif'
Clomial.generate.data: no visible global function definition for
  'rbinom'
Clomial.likelihood: no visible global function definition for 'dbinom'
Phi: no visible global function definition for 'dbinom'
choose.best: no visible global function definition for 'tail'
compute.P.reparam : update.Wj: no visible global function definition
  for 'optim'
compute.P.reparam : plot.obj: no visible global function definition for
  'plot'
compute.q: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom optim plot rbinom runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbinom", "optim", "rbinom", "runif")
  importFrom("utils", "tail")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
choose.best        54.00   1.79   55.80
Clomial            17.47   0.64   18.11
Clomial-package    17.39   0.45   17.84
Clomial.likelihood 12.53   0.55   13.07
Clomial.iterate    11.20   0.60   11.80
compute.bic         8.36   0.39    8.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
choose.best        58.85   1.75   60.60
Clomial            19.62   0.50   20.12
Clomial-package    18.67   0.58   19.25
compute.bic        14.86   0.33   15.18
Clomial.likelihood 10.04   0.34   10.40
Clomial.iterate     9.43   0.25    9.67
compute.errors      5.50   0.28    5.79
* 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/Clomial.Rcheck/00check.log'
for details.


Clomial.Rcheck/00install.out:


install for i386

* installing *source* package 'Clomial' ...
** R
** data
** 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 'Clomial' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clomial' as Clomial_1.12.0.zip
* DONE (Clomial)

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

nameusersystemelapsed
Clomial-package17.39 0.4517.84
Clomial17.47 0.6418.11
Clomial.generate.data0.460.000.45
Clomial.iterate11.2 0.611.8
Clomial.likelihood12.53 0.5513.07
Clomial10000.190.000.19
breastCancer000
choose.best54.00 1.7955.80
compute.bic8.360.398.75
compute.errors4.430.074.50

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

nameusersystemelapsed
Clomial-package18.67 0.5819.25
Clomial19.62 0.5020.12
Clomial.generate.data0.50.00.5
Clomial.iterate9.430.259.67
Clomial.likelihood10.04 0.3410.40
Clomial10000.170.000.17
breastCancer0.000.020.01
choose.best58.85 1.7560.60
compute.bic14.86 0.3315.18
compute.errors5.500.285.79