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BioC 3.4: CHECK report for mdqc on moscato1

This page was generated on 2016-09-21 03:42:26 -0700 (Wed, 21 Sep 2016).

Package 705/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdqc 1.35.0
Gabriela Cohen-Freue
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mdqc
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mdqc
Version: 1.35.0
Command: rm -rf mdqc.buildbin-libdir mdqc.Rcheck && mkdir mdqc.buildbin-libdir mdqc.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mdqc.buildbin-libdir mdqc_1.35.0.tar.gz >mdqc.Rcheck\00install.out 2>&1 && cp mdqc.Rcheck\00install.out mdqc-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mdqc.buildbin-libdir --install="check:mdqc-install.out" --force-multiarch --no-vignettes --timings mdqc_1.35.0.tar.gz
StartedAt: 2016-09-20 11:38:18 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:38:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 38.6 seconds
RetCode: 0
Status:  OK  
CheckDir: mdqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mdqc.buildbin-libdir mdqc.Rcheck && mkdir mdqc.buildbin-libdir mdqc.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mdqc.buildbin-libdir mdqc_1.35.0.tar.gz >mdqc.Rcheck\00install.out 2>&1 && cp mdqc.Rcheck\00install.out mdqc-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mdqc.buildbin-libdir --install="check:mdqc-install.out" --force-multiarch --no-vignettes --timings mdqc_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/mdqc.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 'mdqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mdqc' version '1.35.0'
* 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 'mdqc' 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
Tbsb: no visible global function definition for 'pchisq'
Tbsc: no visible global function definition for 'qchisq'
ksiint: no visible global function definition for 'pgamma'
mdqc: no visible global function definition for 'as.dist'
mdqc: no visible global function definition for 'mahalanobis'
mySm: no visible global function definition for 'var'
mySm: no visible global function definition for 'mahalanobis'
plot.mdqc: no visible global function definition for 'par'
plot.mdqc: no visible global function definition for 'plot'
plot.mdqc: no visible global function definition for 'abline'
plot.mdqc: no visible global function definition for 'qchisq'
plot.mdqc: no visible global function definition for 'points'
plot.mdqc: no visible global function definition for 'text'
print.mdqc: no visible global function definition for 'qchisq'
summary.mdqc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline as.dist mahalanobis par pchisq pgamma plot points qchisq text
  var
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "text")
  importFrom("stats", "as.dist", "mahalanobis", "pchisq", "pgamma",
             "qchisq", "var")
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 ... NOTE
S3 methods shown with full name in documentation object 'prcomp.robust':
  'prcomp.robust'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/mdqc.Rcheck/00check.log'
for details.


mdqc.Rcheck/00install.out:


install for i386

* installing *source* package 'mdqc' ...
** 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 'mdqc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mdqc' as mdqc_1.35.0.zip
* DONE (mdqc)

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

nameusersystemelapsed
allQC0.020.010.03
mdqc2.770.002.78
plot.mdqc0.660.000.66
prcomp.robust0.630.000.63

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

nameusersystemelapsed
allQC0.010.000.02
mdqc3.580.013.70
plot.mdqc0.820.000.82
prcomp.robust0.720.000.78