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@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