Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for Category on zin1

This page was generated on 2016-04-23 10:10:20 -0700 (Sat, 23 Apr 2016).

Package 142/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.36.0
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Category
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Category
Version: 2.36.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.36.0.tar.gz
StartedAt: 2016-04-22 22:48:55 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:51:29 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 154.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Category.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Category.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.36.0’
* 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 ... [11s/11s] 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 ... [17s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [36s/36s]
 [36s/36s] 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
  ‘/home/biocbuild/bbs-3.2-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-class3.8790.0633.946
ChrMapHyperGParams-class0.0010.0000.002
ChrMapHyperGResult-class0.0010.0010.001
ChrMapLinearMParams-class0.0010.0000.001
ChrMapLinearMResult-class0.0010.0000.001
DatPkg-class0.0490.0000.049
HyperGResult-accessors0.7490.0000.918
LinearMResult-class0.0010.0000.001
MAPAmat3.3240.0043.325
applyByCategory0.0040.0000.004
cateGOryMatrix0.2000.0120.236
cb_parse_band_Hs0.0010.0000.001
cb_parse_band_Mm0.0010.0000.001
findAMstats0.0020.0000.001
getPathNames0.0530.0000.053
gseattperm1.1650.0161.181
hyperg0.5100.0040.513
makeChrBandGraph2.1790.0002.178
makeEBcontr0.1270.0000.128
probes2MAP0.1640.0000.165
probes2Path0.0470.0000.047
ttperm0.0110.0040.015