[BioC] Rgraphviz crashes R
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Mon Jun 22 18:53:58 CEST 2009
Hi Sofia
This might not fix all of your problems, but you certainly want to set
these 4 environment variables
> GRAPHVIZ_INSTALL_DIR=
> GRAPHVIZ_INSTALL_MAJOR=
> GRAPHVIZ_INSTALL_MINOR=
> GRAPHVIZ_INSTALL_SUBMINOR=
(what seems to happen is that these variables have no value and sh
complains that you cannot compare to no value, I'll put this on my
todo list).
Instructions on how to do so reside in a README file inside the
Rgraphviz tarball. So you download Rgraphviz, untar it (using
tar xvzf Rgraphviz_*
) and read the text file.
Hmm, I should get around to putting these instructions in the
vignette, this is an awful irritating place to have them. Well, I'll
just copy and paste them below (so ignore the previous paragraph)
Compiling from source on Windows
--------------------------------
If you want to compile Rgraphviz from source you can use any version
of Graphviz you want (but in general, stay away from development
versions). Older version so Graphviz (2.2.1 to say 2.16 might not
work).
o. Install Graphviz as outlined in the previous section
o. Set the following Windows environment variables accordingly
(control panel -> systems -> Advanced -> Environment Variables ):
(a) create new user variables:
GRAPHVIZ_INSTALL_DIR (e.g., C:\/Graphviz-2.22)
GRAPHVIZ_INSTALL_MAJOR (e.g., 2)
GRAPHVIZ_INSTALL_MINOR (e.g., 22)
GRAPHVIZ_INSTALL_SUBMINOR (e.g., 2)
Notice the way "\/" are used for the paths above.
(b) add to user variable 'PATH': %GRAPHVIZ_INSTALL_DIR%/bin
e.g., C:/Graphviz-2.22/bin
o. run "R CMD INSTALL Rgraphviz" or "biocLite("Rgraphviz", type =
"Source")' as usual
Kasper
On Jun 22, 2009, at 5:11 , Sofia Massa wrote:
> 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
>>>>
>>>>
>>>
>>
>>
>
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