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BioC 3.5: CHECK report for Clomial on tokay2

This page was generated on 2017-08-16 13:23:02 -0400 (Wed, 16 Aug 2017).

Package 229/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clomial 1.12.0
Habil Zare
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Clomial
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: 2017-08-15 22:44:34 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:50:14 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 339.7 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 3.4.1 (2017-06-30)
* 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        56.09   2.25   58.34
Clomial            17.89   0.80   18.69
Clomial-package    16.92   0.59   17.52
Clomial.likelihood 12.70   0.36   13.07
Clomial.iterate    11.02   0.47   11.48
compute.bic        10.53   0.36   10.89
compute.errors      5.36   0.20    5.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
choose.best        54.36   1.54   55.89
Clomial            20.78   0.48   21.27
Clomial-package    20.14   0.77   20.91
compute.bic        14.26   0.37   14.64
Clomial.likelihood 10.28   0.30   10.58
Clomial.iterate     9.72   0.28   10.00
compute.errors      7.47   0.27    7.74
* 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-package16.92 0.5917.52
Clomial17.89 0.8018.69
Clomial.generate.data0.530.000.53
Clomial.iterate11.02 0.4711.48
Clomial.likelihood12.70 0.3613.07
Clomial10000.300.000.29
breastCancer0.000.010.02
choose.best56.09 2.2558.34
compute.bic10.53 0.3610.89
compute.errors5.360.205.57

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

nameusersystemelapsed
Clomial-package20.14 0.7720.91
Clomial20.78 0.4821.27
Clomial.generate.data0.50.00.5
Clomial.iterate 9.72 0.2810.00
Clomial.likelihood10.28 0.3010.58
Clomial10000.210.000.20
breastCancer0.000.010.02
choose.best54.36 1.5455.89
compute.bic14.26 0.3714.64
compute.errors7.470.277.74