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 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Category.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [30s/51s] 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
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’
XXXgetUniverseViaGo_db: no visible global function definition for
‘dbGetQuery’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChrBandTree-class 10.981 0.232 11.566
MAPAmat 7.419 0.318 7.742
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [85s/86s]
[85s/86s] 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/Category.Rcheck/00check.log’
for details.