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BioC 3.1: CHECK report for Category on morelia

This page was generated on 2015-10-09 09:38:06 -0700 (Fri, 09 Oct 2015).

Package 136/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.34.2
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Category
Last Changed Rev: 103828 / Revision: 109384
Last Changed Date: 2015-05-14 13:07:36 -0700 (Thu, 14 May 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Category
Version: 2.34.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.34.2.tar.gz
StartedAt: 2015-10-08 23:53:41 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:57:15 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 213.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Category.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.34.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Category.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.34.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘stats4’ ‘Matrix’ ‘BiocGenerics’ ‘AnnotationDbi’ ‘Biobase’ ‘GO.db’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Category’ can be installed ... [14s/14s] 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’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘AnnotationDbi’ ‘graph’ ‘genefilter’
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' calls in package code:
  ‘EBarrays’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GO.db’ ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘DatPkgFactory’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
XXXgetUniverseViaGo_db: no visible global function definition for
  ‘dbGetQuery’
augmentByAncestors: no visible binding for global variable
  ‘GOMFANCESTOR’
augmentByAncestors: no visible binding for global variable
  ‘GOBPANCESTOR’
augmentByAncestors: no visible binding for global variable
  ‘GOCCANCESTOR’
getGoToEntrezMap_db: no visible global function definition for
  ‘dbGetQuery’
getPfamToEntrezMap: no visible global function definition for ‘keys’
getPfamToEntrezMap: no visible global function definition for ‘select’
getUniverseViaKegg_db: no visible global function definition for
  ‘dbGetQuery’
getUniverseViaPfam: no visible global function definition for ‘keys’
getUniverseViaPfam_db: no visible global function definition for
  ‘dbGetQuery’
gseattperm : <anonymous>: no visible global function definition for
  ‘Matrix’
htmlReportFromDf: no visible global function definition for ‘xtable’
makeEBcontr: no visible global function definition for ‘ebPatterns’
GO2AllProbes,Org.XX.egDatPkg: no visible global function definition for
  ‘dbGetQuery’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'organism' and siglist 'DatPkg'
  generic 'organism' and siglist 'GeneSetCollectionDatPkg'
  generic 'organism' and siglist 'HyperGParams'
  generic 'organism' and siglist 'HyperGResult'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  inst/UnitTests/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘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 ... [22s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [57s/58s]
 [57s/58s] 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/Category.Rcheck/00check.log’
for details.


Category.Rcheck/00install.out:

* installing *source* package ‘Category’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Category)

Category.Rcheck/Category-Ex.timings:

nameusersystemelapsed
ChrBandTree-class4.3920.3664.794
ChrMapHyperGParams-class0.0020.0010.003
ChrMapHyperGResult-class0.0010.0000.002
ChrMapLinearMParams-class0.0010.0000.002
ChrMapLinearMResult-class0.0020.0010.002
DatPkg-class0.0630.0010.064
HyperGResult-accessors0.8690.0711.132
LinearMResult-class0.0010.0010.002
MAPAmat3.3670.3193.689
applyByCategory0.0040.0010.005
cateGOryMatrix0.2550.0250.296
cb_parse_band_Hs0.0000.0000.001
cb_parse_band_Mm0.0010.0000.001
findAMstats0.0020.0000.001
getPathNames0.0670.0140.090
gseattperm1.2830.0831.367
hyperg0.5200.0850.604
makeChrBandGraph2.910.323.24
makeEBcontr0.1990.0030.202
probes2MAP0.1940.0010.195
probes2Path0.0630.0010.063
ttperm0.0140.0010.015