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BioC 3.2: CHECK report for graphite on zin1

This page was generated on 2015-08-24 10:48:19 -0700 (Mon, 24 Aug 2015).

Package 452/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.15.1
Gabriele Sales
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graphite
Last Changed Rev: 105076 / Revision: 107696
Last Changed Date: 2015-06-17 07:03:31 -0700 (Wed, 17 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ ERROR ]
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: graphite
Version: 1.15.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graphite_1.15.1.tar.gz
StartedAt: 2015-08-24 00:35:31 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:37:22 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 110.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: graphite.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graphite_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/graphite.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.15.1’
* 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 ‘graphite’ can be installed ... [19s/19s] OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runTopologyGSA,list : .local: no visible binding for global variable
  ‘expr’
runTopologyGSA,list : .local: no visible binding for global variable
  ‘classes’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 32 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘graphite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runClipper
> ### Title: Run a topological analysis on an expression dataset using
> ###   clipper.
> ### Aliases: runClipper runClipper,list-method
> ### Keywords: topology analysis clipper
> 
> ### ** Examples
> 
> if (require(clipper) & require(ALL)){
+   k <- pathways("hsapiens", "kegg")
+   path <- convertIdentifiers(k$'Chronic myeloid leukemia', "entrez")
+   genes <- nodes(path)
+   data(ALL)
+   all <- as.matrix(exprs(ALL[1:length(genes),1:20]))
+   classes <- c(rep(1,10), rep(2,10))
+   rownames(all) <- genes
+   runClipper(path, all, classes, "mean", pathThr=0.1)
+ }
Loading required package: clipper
Loading required package: Matrix
Loading required package: graph
Loading required package: ALL
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Error in moralize.default(graph) : Graph must be directed
Calls: runClipper ... runPathwayVar -> as -> .class1 -> moralize -> moralize.default
Execution halted
* 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: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/graphite.Rcheck/00check.log’
for details.

graphite.Rcheck/00install.out:

* installing *source* package ‘graphite’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘graphite’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graphite)

graphite.Rcheck/graphite-Ex.timings:

nameusersystemelapsed
as.list.DeprecatedPathwayList1.3450.1681.515
as.list.PathwayList0.1160.0160.131
convertIdentifiers0.5330.0080.546
cytoscapePlot0.0010.0000.000
pathwayDatabases0.0140.0000.014
pathwayGraph0.0270.0000.027
pathways0.0010.0000.001