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BioC 2.14: CHECK report for EBarrays on morelia

This page was generated on 2014-10-08 09:02:13 -0700 (Wed, 08 Oct 2014).

Package 245/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBarrays 2.28.0
Ming Yuan
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/EBarrays
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: EBarrays
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBarrays_2.28.0.tar.gz
StartedAt: 2014-10-07 22:33:26 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:34:32 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 65.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: EBarrays.Rcheck
Warnings: 3

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBarrays_2.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBarrays/DESCRIPTION’ ... OK
* this is package ‘EBarrays’ version ‘2.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EBarrays’ can be installed ... [3s/3s] WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck/00_pkg_src/EBarrays/man/emfit.Rd:13-18: Section \synopsis is unrecognized and will be dropped
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘lattice’ ‘methods’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
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 ... WARNING
prepare_Rd: crit.fun.Rd:51: Dropping empty section \keyword
prepare_Rd: ebplots.Rd:116-117: Dropping empty section \examples
prepare_Rd: emfit.Rd:13-18: Section \synopsis is unrecognized and will be dropped
* 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 'emfit':
emfit
  Code: function(data, family, hypotheses, ...)
  Docs: function(data, family, hypotheses, cluster, type = 2, criterion
                 = "BIC", cluster.init = NULL, num.iter = 20, verbose =
                 getOption("verbose"), optim.control = list(), ...)
  Argument names in docs not in code:
    cluster type criterion cluster.init num.iter verbose optim.control
  Mismatches in argument names:
    Position: 4 Code: ... Docs: cluster

* 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 ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [14s/14s]
 [14s/14s] 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 were 3 warnings.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck/00check.log’
for details.

EBarrays.Rcheck/00install.out:

* installing *source* package ‘EBarrays’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ebarrays.c -o ebarrays.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o EBarrays.so ebarrays.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck/EBarrays/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/EBarrays.Rcheck/00_pkg_src/EBarrays/man/emfit.Rd:13-18: Section \synopsis is unrecognized and will be dropped
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBarrays)

EBarrays.Rcheck/EBarrays-Ex.timings:

nameusersystemelapsed
crit.fun4.1460.1374.286
ebarraysFamily-class0.0090.0000.009
emfit0.2300.0090.238
gould0.0090.0010.009
postprob0.2490.0120.261
utilities0.0020.0000.002