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BioC 2.13: CHECK report for GeneticsDesign on moscato1

This page was generated on 2014-04-05 09:49:25 -0700 (Sat, 05 Apr 2014).

Package 293/750HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsDesign 1.30.0
The R Genetics Project
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GeneticsDesign
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GeneticsDesign
Version: 1.30.0
Command: rm -rf GeneticsDesign.buildbin-libdir && mkdir GeneticsDesign.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneticsDesign.buildbin-libdir GeneticsDesign_1.30.0.tar.gz >GeneticsDesign-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GeneticsDesign.buildbin-libdir --install="check:GeneticsDesign-install.out" --force-multiarch --no-vignettes --timings GeneticsDesign_1.30.0.tar.gz && mv GeneticsDesign.buildbin-libdir/* GeneticsDesign.Rcheck/ && rmdir GeneticsDesign.buildbin-libdir
StartedAt: 2014-04-05 04:07:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:07:32 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 27.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneticsDesign.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GeneticsDesign.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsDesign/DESCRIPTION' ... OK
* this is package 'GeneticsDesign' version '1.30.0'
* 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 'GeneticsDesign' 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
* 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 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
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nc' to 'ncol'
pw: warning in matrix(c(1, pi, pi, 1), nr = 2): partial argument match
  of 'nr' to 'nrow'
pw: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2, sd2^2), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(1, pi, pi, 1), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2,
  sd2^2), nr = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... NOTE
prepare_Rd: power.genotype.conti.Rd:36-38: Dropping empty section \details
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GPC.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** running examples for arch 'x64' ... [1s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/GeneticsDesign.Rcheck/00check.log'
for details.

GeneticsDesign.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneticsDesign' ...
** 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 'GeneticsDesign' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneticsDesign' as GeneticsDesign_1.30.0.zip
* DONE (GeneticsDesign)

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

nameusersystemelapsed
GPC0.010.000.01
GeneticPower.Quantitative.Numeric0.020.000.02
gregorius0.010.000.01
power.genotype.conti0.220.000.22

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

nameusersystemelapsed
GPC000
GeneticPower.Quantitative.Numeric000
gregorius0.010.000.01
power.genotype.conti0.130.020.14