paxtoolsr 1.3.1
Augustin Luna
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr | | Last Changed Rev: 104526 / Revision: 107696 | | Last Changed Date: 2015-06-03 11:33:28 -0700 (Wed, 03 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 paxtoolsr_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/paxtoolsr.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 ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.3.1’
* 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 ‘paxtoolsr’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
installed size is 26.6Mb
sub-directories of 1Mb or more:
extdata 4.9Mb
java 21.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘paxtoolsr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: validate
> ### Title: Validate BioPAX files
> ### Aliases: validate
>
> ### ** Examples
>
> outFile <- tempfile()
> rawDoc <- validate(system.file("extdata", "raf_map_kinase_cascade_reactome.owl",
+ package="paxtoolsr"), onlyErrors=TRUE)
9344 [main] ERROR org.biopax.paxtools.PaxtoolsMain - Unable to check with the biopax-validator web service:
org.apache.http.client.HttpResponseException: Found
Fall-back: trying to parse the file(s) with paxtools (up to the first syntax error in each file)...
org.apache.http.client.HttpResponseException: Found
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:47)
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:40)
at org.apache.http.client.fluent.Response.handleResponse(Response.java:85)
at org.apache.http.client.fluent.Response.returnContent(Response.java:92)
at org.biopax.paxtools.client.BiopaxValidatorClient.validate(BiopaxValidatorClient.java:171)
at org.biopax.paxtools.PaxtoolsMain.validate(PaxtoolsMain.java:337)
Start tag expected, '<' not found
Error: 1: Start tag expected, '<' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [13s/13s]
[13s/13s] 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: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.2-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.