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BioC 2.14: CHECK report for RBioinf on morelia

This page was generated on 2014-10-08 09:03:35 -0700 (Wed, 08 Oct 2014).

Package 633/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBioinf 1.24.0
Robert Gentleman
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/RBioinf
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  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: RBioinf
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBioinf_1.24.0.tar.gz
StartedAt: 2014-10-08 01:00:30 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:01:03 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 33.2 seconds
RetCode: 0
Status:  OK 
CheckDir: RBioinf.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBioinf_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RBioinf.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 ‘RBioinf/DESCRIPTION’ ... OK
* this is package ‘RBioinf’ version ‘1.24.0’
* 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 ‘RBioinf’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘graph’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘methods:::.getMethodsTable’
  See the note in ?`:::` about the use of this operator.
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 ... NOTE
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
  match of 'nr' to 'nrow'
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
  match of 'nc' to 'ncol'
* 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 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 ... NOTE
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/RBioinf.Rcheck/RBioinf/libs/RBioinf.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘rand.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/RBioinf.Rcheck/00check.log’
for details.

RBioinf.Rcheck/00install.out:

* installing *source* package ‘RBioinf’ ...
** 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 Rinit.c -o Rinit.o
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 rand.c -o rand.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o RBioinf.so Rinit.o rand.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/RBioinf.Rcheck/RBioinf/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RBioinf)

RBioinf.Rcheck/RBioinf-Ex.timings:

nameusersystemelapsed
Rcal0.0130.0130.122
S4Help0.0010.0000.000
asSimpleVector0.0000.0000.001
classList2Graph0.2190.0030.223
computeClassLinearization0.0820.0010.082
printWithNumbers0.0010.0000.002
randDNA0.0010.0000.001
simplePVect0.0010.0010.000
simpleRand0.0010.0000.001
simpleSort0.0010.0000.000
subClassNames0.0010.0010.001
superClasses0.0000.0000.001
traceMethods0.0010.0000.000