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BioC 2.13: CHECK report for girafe on perceval

This page was generated on 2014-04-05 09:52:25 -0700 (Sat, 05 Apr 2014).

Package 310/750HostnameOS / ArchBUILDCHECKBUILD BIN
girafe 1.14.0
J. Toedling
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/girafe
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: girafe
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch girafe_1.14.0.tar.gz
StartedAt: 2014-04-05 01:39:30 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:45:49 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 379.5 seconds
RetCode: 0
Status:  OK 
CheckDir: girafe.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/girafe.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 ‘girafe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘girafe’ version ‘1.14.0’
* 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 ‘girafe’ can be installed ... [33s/34s] OK
* 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:
  ‘methods’ ‘IRanges’ ‘genomeIntervals’
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 ‘Rsamtools’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘MASS:::fitdistr’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘genomeIntervals:::intervalsForOverlap’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getChromLengths’
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
countReadsAnnotated: no visible binding for global variable ‘fraction1’
fracOverlap: no visible binding for global variable ‘fraction1’
fracOverlap: no visible binding for global variable ‘fraction2’
getFeatureCounts: no visible binding for global variable ‘fraction1’
getFeatureCounts: no visible binding for global variable ‘Index1’
reduceOne: no visible binding for global variable ‘fraction1’
reduceOne: no visible binding for global variable ‘fraction2’
windowCountAndGC: no visible binding for global variable ‘n.reads’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘girafe.tex’, ‘Makefile’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘girafe.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [68s/68s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
negbinomsig                  20.225  0.167  20.664
perWindow                    18.223  0.127  18.589
AlignedGenomeIntervals-class  7.840  0.240   8.136
* 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 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/girafe.Rcheck/00check.log’
for details.

girafe.Rcheck/00install.out:

* installing *source* package ‘girafe’ ...
** 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 coverage.cpp -o coverage.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c girafe_init.c -o girafe_init.o
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 girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/girafe.Rcheck/girafe/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘girafe’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
* DONE (girafe)

girafe.Rcheck/girafe-Ex.timings:

nameusersystemelapsed
AlignedGenomeIntervals-class7.8400.2408.136
agiFromBam0.4790.0450.525
countReadsAnnotated0.2100.0080.217
fracOverlap0.2090.0070.216
intPhred0.0830.0080.091
medianByPosition2.1350.0482.192
negbinomsig20.225 0.16720.664
perWindow18.223 0.12718.589
plotAligned0.0820.0090.091
trimAdapter0.1330.0110.146
weightedConsensusMatrix0.0230.0080.034
whichNearestMethods1.1480.0241.185