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BioC 3.0: CHECK report for Category on zin1

This page was generated on 2015-04-10 09:37:04 -0700 (Fri, 10 Apr 2015).

Package 126/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.32.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Category
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: Category
Version: 2.32.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.32.0.tar.gz
StartedAt: 2015-04-09 22:14:47 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:18:47 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 239.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Category.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Category.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.32.0’
* 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 ... [19s/19s] 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 ... 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/26s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ChrBandTree-class 5.62  0.048   5.674
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/46s]
 [46s/46s] 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/Category.Rcheck/00check.log’
for details.

Category.Rcheck/00install.out:

* installing *source* package ‘Category’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Category)

Category.Rcheck/Category-Ex.timings:

nameusersystemelapsed
ChrBandTree-class5.6200.0485.674
ChrMapHyperGParams-class0.0040.0000.001
ChrMapHyperGResult-class0.0000.0000.001
ChrMapLinearMParams-class0.0000.0000.001
ChrMapLinearMResult-class0.0000.0000.001
DatPkg-class0.0560.0080.066
HyperGResult-accessors0.9760.0121.086
LinearMResult-class0.0000.0000.001
MAPAmat4.3610.0164.383
applyByCategory0.0040.0000.006
cateGOryMatrix0.2120.0120.228
cb_parse_band_Hs0.0000.0000.001
cb_parse_band_Mm0.0040.0000.001
findAMstats0.0040.0000.002
getPathNames0.080.000.08
gseattperm1.5160.0401.559
hyperg0.5880.0040.595
makeChrBandGraph2.6440.0002.647
makeEBcontr0.2120.0160.231
probes2MAP0.1880.0000.189
probes2Path0.0640.0080.073
ttperm0.0200.0000.018