Error in re-building vignettes:
  ...
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

The following object is masked from ‘package:base’:

    isNamespaceLoaded

Loading required package: rjson
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*                                        *

*          Welcome to WebGestaltR !      *

*                                        *

******************************************

trying URL 'http://www.webgestalt.org//data/xref/hsapiens_genesymbol.table'
Content type 'unknown' length 1039725 bytes (1015 KB)
==================================================
downloaded 1015 KB

trying URL 'http://www.webgestalt.org//data/xref/hsapiens_genesymbol.table'
Content type 'unknown' length 1039725 bytes (1015 KB)
==================================================
downloaded 1015 KB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_BiologicalProcess.table'
Content type 'unknown' length 2519935 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_CellularComponent.table'
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://www.webgestalt.org//js/plotDAG.js'
Content type 'text/javascript' length 2860 bytes
==================================================
downloaded 2860 bytes

trying URL 'http://www.webgestalt.org//js/xtrace_utils.js'
Content type 'text/javascript' length 13665 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'http://www.webgestalt.org//js/xtrace_graph.js'
Content type 'text/javascript' length 13410 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'http://www.webgestalt.org//data/xref/hsapiens_genesymbol.table'
Content type 'unknown' length 1039725 bytes (1015 KB)
==================================================
downloaded 1015 KB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_BiologicalProcess.table'
Content type 'unknown' length 2519935 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_CellularComponent.table'
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org//data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://www.webgestalt.org//gsea.jar'
Content type 'application/x-java-archive' length 12356152 bytes (11.8 MB)
==================================================
downloaded 11.8 MB

5155 [INFO ] Made Vdb dir JIT: /data/gannet/ripley/R/packages/tests-devel/WebGestaltR.Rcheck/vign_test/WebGestaltR/vignettes/feb26
java.io.IOException: Specified path is a Directory (expecting a File): /data/gannet/ripley/R/packages/tests
	at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:2638)
	at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:1971)
	at xtools.api.param.PobParam.getPob(PobParam.java:134)
	at xtools.api.param.RankedListReqdParam.getRankedList(RankedListReqdParam.java:50)
	at xtools.gsea.GseaPreranked.createHeader(GseaPreranked.java:158)
	at xtools.gsea.GseaPreranked.execute(GseaPreranked.java:65)
	at xtools.api.AbstractTool.tool_main(AbstractTool.java:620)
	at xtools.gsea.GseaPreranked.main(GseaPreranked.java:152)
java.io.IOException: Specified path is a Directory (expecting a File): /data/gannet/ripley/R/packages/tests
	at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:2638)
	at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:1971)
	at xtools.api.param.PobParam.getPob(PobParam.java:134)
	at xtools.api.param.RankedListReqdParam.getRankedList(RankedListReqdParam.java:50)
	at xtools.gsea.GseaPreranked.execute(GseaPreranked.java:68)
	at xtools.api.AbstractTool.tool_main(AbstractTool.java:620)
	at xtools.gsea.GseaPreranked.main(GseaPreranked.java:152)
5627 [INFO ] Renaming rpt dir on error to: /data/gannet/ripley/R/packages/tests/error_Project_1488125529_30037.GseaPreranked.1488125555302

Error: processing vignette 'WebGestaltR.Rnw' failed with diagnostics:
 chunk 1 (label = Example) 
Error in fread(input = positiveF, header = TRUE, sep = "\t", stringsAsFactors = FALSE,  : 
  'input' must be a single character string containing a file name, a command, full path to a file, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or the input data itself
Execution halted