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BioC 2.13: CHECK report for dexus on perceval

This page was generated on 2014-04-05 09:53:03 -0700 (Sat, 05 Apr 2014).

Package 202/750HostnameOS / ArchBUILDCHECKBUILD BIN
dexus 1.2.2
Guenter Klambauer
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/dexus
Last Changed Rev: 85162 / Revision: 88450
Last Changed Date: 2013-12-30 05:50:04 -0800 (Mon, 30 Dec 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: dexus
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dexus_1.2.2.tar.gz
StartedAt: 2014-04-05 00:51:13 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:53:29 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 136.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: dexus.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/dexus.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.2.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dexus’ can be installed ... [4s/38s] 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
* 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 ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'dexus':
dexus
  Code: function(X, nclasses = 2, alphaInit, G = 1, cyc = 20, labels =
                 NULL, normalization = "RLE", kmeansIter = 10,
                 ignoreIfAllCountsSmaller = 1, theta = 2.5, minMu =
                 0.5, rmax = 13, initialization = "kmeans",
                 multiclassPhiPoolingFunction = NULL, quiet = FALSE,
                 resultObject = "S4")
  Docs: function(X, nclasses = 2, alphaInit = c(0.5, 0.5), G = 1, cyc =
                 20, labels = NULL, normalization = "RLE", kmeansIter =
                 10, ignoreIfAllCountsSmaller = 1, theta = 2.5, minMu =
                 0.5, rmax = 13, initialization = "kmeans",
                 multiclassPhiPoolingFunction = NULL, quiet = FALSE,
                 resultObject = "S4")
  Mismatches in argument default values:
    Name: 'alphaInit' Code:  Docs: c(0.5, 0.5)

* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/dexus.Rcheck/00check.log’
for details.

dexus.Rcheck/00install.out:

* installing *source* package ‘dexus’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c dexus.cpp -o dexus.o
dexus.cpp: In function ‘SEXPREC* dexus_impl(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, int*, SEXPREC*, SEXPREC*, SEXPREC*)’:
dexus.cpp:193: warning: unused variable ‘DEFAULT_R’
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o dexus.so dexus.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/dexus.Rcheck/dexus/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘dexus’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)

dexus.Rcheck/dexus-Ex.timings:

nameusersystemelapsed
DEXUSResult-class0.0120.0000.012
DEXUSResult-subset2.3540.1232.493
INI1.5790.0721.723
INIThreshold-set1.1060.0871.210
accessors1.3520.0991.530
dexus0.9150.0571.003
dexus.parallel0.9270.0610.991
getSizeNB0.0340.0020.036
normalizeData2.1060.1762.282
plot1.3980.0671.478
sort1.3770.0691.448