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