[BioC] Problems with getBioC (reposTools, really) and package Rgraphviz

[Rafal Kustra]

when trying to run getBioC (or just library(reposTools) after installing
it manually), I was getting:

getBioC(verbose=TRUE)
Running getBioC version 1.2.38....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
 
Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.
 
[1] "Installing reposTools ..."
Creating a new generic function for "summary" in package
reposTools
 
Synching your local package management information ...
Error in if (e1[i] != e2[i]) return(TRUE) :
        missing value where TRUE/FALSE needed
Error in library(reposTools) : .First.lib failed



I changed the tests in reposTools R script (around lines 3451 and 3461)
to:
if (is.na(e1[i]) || is.na(e2[i]) || e1[i] != e2[i])

which I'm pretty sure is an ugly hack but it made getBioC work.



For package Rgraphviz I had compilation errors

ote: No specified download type, defaulting to Source 
[1] "Attempting to download Rgraphviz from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing Rgraphviz"
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/usr/lib/R/include `dotneato-config --cflags` 
-I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -O2 -g
-pipe -march=i686 -c Rgraphviz.c -o Rgraphviz.o
/bin/sh: line 1: dotneato-config: command not found
In file included from Rgraphviz.c:1:
common.h:19:20: render.h: No such file or directory
common.h:20:19: graph.h: No such file or directory
common.h:21:22: dotprocs.h: No such file or directory
common.h:22:24: neatoprocs.h: No such file or directory
common.h:23:20: adjust.h: No such file or directory
In file included from Rgraphviz.c:1:
common.h:37: parse error before '*' token
common.h:38: parse error before '*' token
common.h:41: parse error before '*' token
common.h:42: parse error before '*' token
common.h:44: parse error before '*' token
common.h:44: parse error before '*' token
common.h:44: warning: type defaults to `int' in declaration of
`dotLayout'
common.h:44: warning: data definition has no type or storage class
common.h:45: parse error before '*' token
common.h:45: parse error before '*' token
common.h:45: warning: type defaults to `int' in declaration of
`neatoLayout'
common.h:45: warning: data definition has no type or storage class
common.h:46: parse error before '*' token
common.h:46: parse error before '*' token
common.h:46: warning: type defaults to `int' in declaration of
`twopiLayout'
common.h:46: warning: data definition has no type or storage class
common.h:47: parse error before '*' token
common.h:47: parse error before '*' token
common.h:47: warning: type defaults to `int' in declaration of
`setDefaultAttrs'
common.h:47: warning: data definition has no type or storage class
Rgraphviz.c:2:20: circle.h: No such file or directory
Rgraphviz.c: In function `Rgraphviz_fin':
Rgraphviz.c:63: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:63: (Each undeclared identifier is reported only once
Rgraphviz.c:63: for each function it appears in.)
Rgraphviz.c:63: `g' undeclared (first use in this function)
Rgraphviz.c:67: warning: implicit declaration of function `agclose'
Rgraphviz.c: In function `Rgraphviz_agset':
Rgraphviz.c:73: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:73: `g' undeclared (first use in this function)
Rgraphviz.c:92: warning: implicit declaration of function `agraphattr'
Rgraphviz.c:100: warning: implicit declaration of function `agnodeattr'
Rgraphviz.c: In function `Rgraphviz_agread':
Rgraphviz.c:111: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:111: `g' undeclared (first use in this function)
Rgraphviz.c:118: warning: implicit declaration of function `aginit'
Rgraphviz.c:119: warning: implicit declaration of function `agread'
Rgraphviz.c: In function `Rgraphviz_agwrite':
Rgraphviz.c:124: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:124: `g' undeclared (first use in this function)
Rgraphviz.c:136: warning: implicit declaration of function `agwrite'
Rgraphviz.c: In function `Rgraphviz_agopen':
Rgraphviz.c:145: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:145: `g' undeclared (first use in this function)
Rgraphviz.c:146: `Agnode_t' undeclared (first use in this function)
Rgraphviz.c:146: `head' undeclared (first use in this function)
Rgraphviz.c:146: `tail' undeclared (first use in this function)
Rgraphviz.c:146: `tmp' undeclared (first use in this function)
Rgraphviz.c:146: warning: left-hand operand of comma expression has no
effect
Rgraphviz.c:146: warning: left-hand operand of comma expression has no
effect
Rgraphviz.c:147: `Agedge_t' undeclared (first use in this function)
Rgraphviz.c:147: `curEdge' undeclared (first use in this function)
Rgraphviz.c:163: warning: implicit declaration of function `agopen'
Rgraphviz.c:170: warning: implicit declaration of function `agnode'
Rgraphviz.c:171: warning: implicit declaration of function `agset'
Rgraphviz.c:177: warning: implicit declaration of function `agfindnode'
Rgraphviz.c:186: warning: implicit declaration of function `agfindedge'
Rgraphviz.c:186: warning: comparison between pointer and integer
Rgraphviz.c:187: warning: implicit declaration of function `agedge'
Rgraphviz.c:191: `AGDIGRAPH' undeclared (first use in this function)
Rgraphviz.c: In function `Rgraphviz_doLayout':
Rgraphviz.c:202: `Agraph_t' undeclared (first use in this function)
Rgraphviz.c:202: `g' undeclared (first use in this function)
Rgraphviz.c:220: warning: implicit declaration of function `dot_layout'
Rgraphviz.c:223: warning: implicit declaration of function
`neato_layout'
Rgraphviz.c:226: warning: implicit declaration of function
`twopi_layout'
Rgraphviz.c: At top level:
Rgraphviz.c:247: parse error before '*' token
Rgraphviz.c: In function `buildRagraph':
Rgraphviz.c:251: `g' undeclared (first use in this function)
Rgraphviz.c:259: warning: implicit declaration of function `agnedges'
Rgraphviz.c: At top level:
Rgraphviz.c:267: parse error before '*' token
Rgraphviz.c: In function `getBoundBox':
Rgraphviz.c:277: `g' undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:289: parse error before '*' token
Rgraphviz.c: In function `getNodeLayouts':
Rgraphviz.c:290: `Agnode_t' undeclared (first use in this function)
Rgraphviz.c:290: `node' undeclared (first use in this function)
Rgraphviz.c:294: `g' undeclared (first use in this function)
Rgraphviz.c:300: warning: implicit declaration of function `agnnodes'
Rgraphviz.c:301: warning: implicit declaration of function `agfstnode'
Rgraphviz.c:315: warning: implicit declaration of function `agnxtnode'
Rgraphviz.c: At top level:
Rgraphviz.c:323: parse error before '*' token
Rgraphviz.c: In function `getEdgeLocs':
Rgraphviz.c:326: `Agnode_t' undeclared (first use in this function)
Rgraphviz.c:326: `node' undeclared (first use in this function)
Rgraphviz.c:326: `head' undeclared (first use in this function)
Rgraphviz.c:326: warning: left-hand operand of comma expression has no
effect
Rgraphviz.c:327: `Agedge_t' undeclared (first use in this function)
Rgraphviz.c:327: `edge' undeclared (first use in this function)
Rgraphviz.c:328: `bezier' undeclared (first use in this function)
Rgraphviz.c:328: parse error before "bez"
Rgraphviz.c:337: `numEdges' undeclared (first use in this function)
Rgraphviz.c:339: `g' undeclared (first use in this function)
Rgraphviz.c:343: warning: implicit declaration of function `agfstout'
Rgraphviz.c:346: `bez' undeclared (first use in this function)
Rgraphviz.c:400: warning: implicit declaration of function `agnxtout'
Rgraphviz.c: In function `checkGraphvizVers':
Rgraphviz.c:415: `Info' undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:424: parse error before '*' token
Rgraphviz.c:424: parse error before '*' token
Rgraphviz.c:424: warning: return type defaults to `int'
Rgraphviz.c: In function `setDefaultAttrs':
Rgraphviz.c:433: `g' undeclared (first use in this function)
Rgraphviz.c:438: `NODENAME_ESC' undeclared (first use in this function)
Rgraphviz.c:445: warning: implicit declaration of function
`AG_IS_DIRECTED'
Rgraphviz.c:446: warning: implicit declaration of function `agedgeattr'
Rgraphviz.c: At top level:
Rgraphviz.c:462: parse error before '*' token
Rgraphviz.c:462: parse error before '*' token
Rgraphviz.c:462: warning: return type defaults to `int'
Rgraphviz.c: In function `dotLayout':
Rgraphviz.c:463: warning: implicit declaration of function
`dot_init_graph'
Rgraphviz.c:463: `g' undeclared (first use in this function)
Rgraphviz.c:464: warning: implicit declaration of function `dot_rank'
Rgraphviz.c:465: warning: implicit declaration of function
`dot_mincross'
Rgraphviz.c:466: warning: implicit declaration of function
`dot_position'
Rgraphviz.c:467: warning: implicit declaration of function
`dot_sameports'
Rgraphviz.c:468: warning: implicit declaration of function `dot_splines'
Rgraphviz.c:469: warning: implicit declaration of function
`dotneato_postprocess'
Rgraphviz.c:469: `dot_nodesize' undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:474: parse error before '*' token
Rgraphviz.c:474: parse error before '*' token
Rgraphviz.c:474: warning: return type defaults to `int'
Rgraphviz.c: In function `neatoLayout':
Rgraphviz.c:477: `attrsym_t' undeclared (first use in this function)
Rgraphviz.c:477: `sym' undeclared (first use in this function)
Rgraphviz.c:479: warning: implicit declaration of function `agfindattr'
Rgraphviz.c:479: `g' undeclared (first use in this function)
Rgraphviz.c:481: warning: implicit declaration of function `agxset'
Rgraphviz.c:486: warning: implicit declaration of function
`neato_init_graph'
Rgraphviz.c:487: warning: implicit declaration of function `scan_graph'
Rgraphviz.c:488: warning: implicit declaration of function `agget'
Rgraphviz.c:488: warning: assignment makes pointer from integer without
a cast
Rgraphviz.c:489: warning: implicit declaration of function `streq'
Rgraphviz.c:490: warning: implicit declaration of function
`circuit_model'
Rgraphviz.c:492: warning: implicit declaration of function
`shortest_path'
Rgraphviz.c:493: warning: implicit declaration of function
`initial_positions'
Rgraphviz.c:494: warning: implicit declaration of function
`diffeq_model'
Rgraphviz.c:495: warning: implicit declaration of function `solve_model'
Rgraphviz.c:496: warning: implicit declaration of function
`final_energy'
Rgraphviz.c:497: warning: implicit declaration of function `adjustNodes'
Rgraphviz.c:498: warning: implicit declaration of function
`spline_edges'
Rgraphviz.c:499: `dot_nodesize' undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:503: parse error before '*' token
Rgraphviz.c:503: parse error before '*' token
Rgraphviz.c:503: warning: return type defaults to `int'
Rgraphviz.c: In function `twopiLayout':
Rgraphviz.c:504: `Agnode_t' undeclared (first use in this function)
Rgraphviz.c:504: `ctr' undeclared (first use in this function)
Rgraphviz.c:506: warning: implicit declaration of function
`twopi_init_graph'
Rgraphviz.c:506: `g' undeclared (first use in this function)
Rgraphviz.c:508: warning: implicit declaration of function
`circleLayout'
Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this
function)
make: *** [Rgraphviz.o] Error 1
ERROR: compilation failed for package 'Rgraphviz'



There was also an error with package rhdf5:

configure: error: please specify a valid hdf5 installation with
--with-hdf5=DIR
ERROR: configuration failed for package 'rhdf5'

Hope it helps,

rafal