[BioC] Rgraphviz crashes R

Mon Jun 22 14:11:31 CEST 2009

Dear Kasper,

Thank you for your suggestions. These are the errors that I get when
installing Rgraphviz from source. Do you have any advice?

Thanks

Sofia

> biocLite("Rgraphviz", type = "source")
Running biocinstall version 2.4.11 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'C:\Users\Sofia\Documents/R/win-library/2.9'
provo con l'URL
'http://bioconductor.org/packages/2.4/bioc/src/contrib/Rgraphviz_1.22.1.tar.gz'
Content type 'application/x-gzip' length 569867 bytes (556 Kb)
URL aperto
downloaded 556 Kb

*** 'hhc.exe' not found: not building CHM help

* Installing *source* package 'Rgraphviz' ...
Using the following environment variables
GRAPHVIZ_INSTALL_DIR=
GRAPHVIZ_INSTALL_MAJOR=
GRAPHVIZ_INSTALL_MINOR=
GRAPHVIZ_INSTALL_SUBMINOR=
test: 2: unknown operand
test: 2: unknown operand
test: 2: unknown operand
Using the following compilation and linking flags for Rgraphviz
   PKG_CPPFLAGS=-I/include/graphviz
   PKG_LIBS=-L/bin -lgvc -lgraph -lcdt
   GVIZ_DEFS=-DGRAPHVIZ_MAJOR= -DGRAPHVIZ_MINOR= -DWin32
Created file src/Makevars.win
Created file R/graphviz_build_version.R
** libs
  making DLL ...
gcc -I"C:/PROGRA~1/R/R-29~1.0/include" -I/include/graphviz
-DGRAPHVIZ_MAJOR= -DGRAPHVIZ_MINOR= -DWin32       -O3 -Wall  -std=gnu99 -c
LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:
common.h:17:20: error: operator '==' has no left operand
In file included from LL_funcs.c:1:
common.h:52: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
common.h:55:20: error: operator '==' has no left operand
common.h:60: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
In file included from LL_funcs.c:2:
util.h:18: error: expected ')' before '*' token
LL_funcs.c:5: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
LL_funcs.c:15: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
LL_funcs.c: In function 'getDefAttrs':
LL_funcs.c:31: error: 'Agdict_t' undeclared (first use in this function)
LL_funcs.c:31: error: (Each undeclared identifier is reported only once
LL_funcs.c:31: error: for each function it appears in.)
LL_funcs.c:31: error: 'dict' undeclared (first use in this function)
LL_funcs.c:31: warning: implicit declaration of function 'agdictof'
LL_funcs.c:34: warning: implicit declaration of function 'dtsize'
LL_funcs.c:47:20: error: operator '==' has no left operand
LL_funcs.c: In function 'Rgraphviz_getDefAttrsGraph':
LL_funcs.c:86: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:86: error: 'g' undeclared (first use in this function)
LL_funcs.c:86: warning: implicit declaration of function 'getAgraphPtr'
LL_funcs.c: In function 'Rgraphviz_setDefAttrsGraph':
LL_funcs.c:113: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:113: error: 'g' undeclared (first use in this function)
LL_funcs.c:118: error: 'Agsym_t' undeclared (first use in this function)
LL_funcs.c:118: error: 'r' undeclared (first use in this function)
LL_funcs.c:118: warning: implicit declaration of function 'agraphattr'
LL_funcs.c: In function 'Rgraphviz_getAttrsGraph':
LL_funcs.c:130: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:130: error: 'g' undeclared (first use in this function)
LL_funcs.c:134: warning: implicit declaration of function 'agget'
LL_funcs.c:134: warning: initialization makes pointer from integer without
a cast
LL_funcs.c: In function 'Rgraphviz_setAttrsGraph':
LL_funcs.c:154: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:154: error: 'g' undeclared (first use in this function)
LL_funcs.c:161: warning: implicit declaration of function 'agsafeset'
LL_funcs.c: In function 'Rgraphviz_getAttrsCluster':
LL_funcs.c:173: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:173: error: 'sg' undeclared (first use in this function)
LL_funcs.c:173: warning: implicit declaration of function 'getClusterPtr'
LL_funcs.c:177: warning: initialization makes pointer from integer without
a cast
LL_funcs.c: In function 'Rgraphviz_setAttrsCluster':
LL_funcs.c:197: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:197: error: 'sg' undeclared (first use in this function)
LL_funcs.c: In function 'Rgraphviz_getDefAttrsNode':
LL_funcs.c:216: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:216: error: 'g' undeclared (first use in this function)
LL_funcs.c:219: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:219: error: 'n' undeclared (first use in this function)
LL_funcs.c: In function 'Rgraphviz_setDefAttrsNode':
LL_funcs.c:244: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:244: error: 'g' undeclared (first use in this function)
LL_funcs.c:249: error: 'Agsym_t' undeclared (first use in this function)
LL_funcs.c:249: error: 'r' undeclared (first use in this function)
LL_funcs.c:249: warning: implicit declaration of function 'agnodeattr'
LL_funcs.c: In function 'Rgraphviz_getAttrsNode':
LL_funcs.c:261: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:261: error: 'g' undeclared (first use in this function)
LL_funcs.c:265: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:265: error: 'n' undeclared (first use in this function)
LL_funcs.c:265: warning: implicit declaration of function 'agfindnode'
LL_funcs.c:270: warning: initialization makes pointer from integer without
a cast
LL_funcs.c: In function 'Rgraphviz_setAttrsNode':
LL_funcs.c:290: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:290: error: 'g' undeclared (first use in this function)
LL_funcs.c:294: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:294: error: 'n' undeclared (first use in this function)
LL_funcs.c: In function 'Rgraphviz_getDefAttrsEdge':
LL_funcs.c:313: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:313: error: 'g' undeclared (first use in this function)
LL_funcs.c:316: error: 'Agedge_t' undeclared (first use in this function)
LL_funcs.c:316: error: 'e' undeclared (first use in this function)
LL_funcs.c: In function 'Rgraphviz_setDefAttrsEdge':
LL_funcs.c:341: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:341: error: 'g' undeclared (first use in this function)
LL_funcs.c:346: error: 'Agsym_t' undeclared (first use in this function)
LL_funcs.c:346: error: 'r' undeclared (first use in this function)
LL_funcs.c:346: warning: implicit declaration of function 'agedgeattr'
LL_funcs.c: In function 'Rgraphviz_getAttrsEdge':
LL_funcs.c:358: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:358: error: 'g' undeclared (first use in this function)
LL_funcs.c:363: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:363: error: 'u' undeclared (first use in this function)
LL_funcs.c:366: error: 'v' undeclared (first use in this function)
LL_funcs.c:370: error: 'Agedge_t' undeclared (first use in this function)
LL_funcs.c:370: error: 'e' undeclared (first use in this function)
LL_funcs.c:370: warning: implicit declaration of function 'agfindedge'
LL_funcs.c:374: warning: initialization makes pointer from integer without
a cast
LL_funcs.c: In function 'Rgraphviz_setAttrsEdge':
LL_funcs.c:394: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:394: error: 'g' undeclared (first use in this function)
LL_funcs.c:399: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:399: error: 'u' undeclared (first use in this function)
LL_funcs.c:402: error: 'v' undeclared (first use in this function)
LL_funcs.c:406: error: 'Agedge_t' undeclared (first use in this function)
LL_funcs.c:406: error: 'e' undeclared (first use in this function)
LL_funcs.c:424:20: error: operator '==' has no left operand
LL_funcs.c: In function 'Rgraphviz_agopenSimple':
LL_funcs.c:462: error: 'Agraph_t' undeclared (first use in this function)
LL_funcs.c:462: error: 'g' undeclared (first use in this function)
LL_funcs.c:462: error: 'tmpGraph' undeclared (first use in this function)
LL_funcs.c:462: warning: left-hand operand of comma expression has no effect
LL_funcs.c:463: error: 'sgs' undeclared (first use in this function)
LL_funcs.c:464: error: 'Agnode_t' undeclared (first use in this function)
LL_funcs.c:464: error: 'head' undeclared (first use in this function)
LL_funcs.c:464: error: 'tail' undeclared (first use in this function)
LL_funcs.c:464: warning: left-hand operand of comma expression has no effect
LL_funcs.c:464: error: 'curNode' undeclared (first use in this function)
LL_funcs.c:464: warning: left-hand operand of comma expression has no effect
LL_funcs.c:465: error: 'Agedge_t' undeclared (first use in this function)
LL_funcs.c:465: error: 'curEdge' undeclared (first use in this function)
LL_funcs.c:490: warning: implicit declaration of function 'aginit'
LL_funcs.c:492: warning: implicit declaration of function 'agopen'
LL_funcs.c:496: error: expected expression before ')' token
LL_funcs.c:510: warning: implicit declaration of function 'agsubg'
LL_funcs.c:535: warning: implicit declaration of function 'agnode'
LL_funcs.c:565: warning: implicit declaration of function 'agedge'
LL_funcs.c:569: warning: implicit declaration of function 'buildRagraph'
LL_funcs.c:569: warning: return makes pointer from integer without a cast
make: *** [LL_funcs.o] Error 1
  ... done
ERROR: compilation failed for package 'Rgraphviz'

> Please keep this on the list.
>
> If you compile from source, Graphviz 2.23 will (or at least "ought
> to") work. Otherwise it won't.
>
> In order to setup your system to compile from source you will need to
> install the Rtools stuff from
>    http://www.murdoch-sutherland.com/Rtools/
>
> You should then be able to install from source by doing
>    biocLite("Rgraphviz", type = "source")
>
> Kasper
>
> On Jun 16, 2009, at 3:04 , Sofia Massa wrote:
>
>> Thank you for the reply. I've tried to use the version 2.23 of
>> Graphviz
>> but it doesn't have the libgvc-4.dll file, so only the version 2.20
>> seems
>> fine.
>>
>> Sorry to ask this, but what should I do to compile Rgraphviz from
>> source?
>>
>> Thanks again,
>>
>> Sofia
>>
>>
>>> You will need to use the development version of Graphviz (version
>>> 2.23.something) and you will need to compile Rgraphviz yourself from
>>> source.
>>>
>>> Kasper
>>>
>>> On Jun 15, 2009, at 14:30 , Sofia Massa wrote:
>>>
>>>> Hello,
>>>>
>>>> I'm having the same problem with Vista and Rgraphviz. The
>>>> installation is
>>>> fine but then R crashes when using a plot command. I haven't seen
>>>> any
>>>> reply to this post. Does anyone has a suggestion for it?
>>>>
>>>> Thank you in advance
>>>>
>>>> Sofia
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>
>