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BioC 3.4: CHECK report for Clomial on moscato1

This page was generated on 2016-09-21 03:45:36 -0700 (Wed, 21 Sep 2016).

Package 207/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clomial 1.9.4
Habil Zare
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Clomial
Last Changed Rev: 118184 / Revision: 121152
Last Changed Date: 2016-06-04 15:55:29 -0700 (Sat, 04 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: Clomial
Version: 1.9.4
Command: rm -rf Clomial.buildbin-libdir Clomial.Rcheck && mkdir Clomial.buildbin-libdir Clomial.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clomial.buildbin-libdir Clomial_1.9.4.tar.gz >Clomial.Rcheck\00install.out 2>&1 && cp Clomial.Rcheck\00install.out Clomial-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Clomial.buildbin-libdir --install="check:Clomial-install.out" --force-multiarch --no-vignettes --timings Clomial_1.9.4.tar.gz
StartedAt: 2016-09-20 05:50:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:53:21 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 175.3 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clomial.buildbin-libdir Clomial_1.9.4.tar.gz >Clomial.Rcheck\00install.out 2>&1 && cp Clomial.Rcheck\00install.out Clomial-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Clomial.buildbin-libdir --install="check:Clomial-install.out" --force-multiarch --no-vignettes --timings Clomial_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Clomial.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.9.4'
* 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        25.90      0   25.89
Clomial             8.20      0    8.21
Clomial-package     8.07      0    8.07
Clomial.iterate     5.18      0    5.17
Clomial.likelihood  5.13      0    5.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
choose.best        29.55   0.00   29.55
Clomial-package    12.04   0.00   12.08
Clomial            11.89   0.00   11.88
compute.bic         6.93   0.02    6.94
Clomial.likelihood  5.29   0.00    5.29
Clomial.iterate     5.15   0.00    5.15
* 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
  'D:/biocbld/bbs-3.4-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_1.9.4.zip
* DONE (Clomial)

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

nameusersystemelapsed
Clomial-package8.070.008.07
Clomial8.200.008.21
Clomial.generate.data0.450.000.45
Clomial.iterate5.180.005.17
Clomial.likelihood5.130.005.14
Clomial10000.270.000.26
breastCancer000
choose.best25.90 0.0025.89
compute.bic4.550.004.56
compute.errors2.480.002.48

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

nameusersystemelapsed
Clomial-package12.04 0.0012.08
Clomial11.89 0.0011.88
Clomial.generate.data0.560.010.58
Clomial.iterate5.150.005.15
Clomial.likelihood5.290.005.29
Clomial10000.300.000.29
breastCancer000
choose.best29.55 0.0029.55
compute.bic6.930.026.94
compute.errors3.540.003.55