Subscribing to the Mac SIG mailing list might also be a good idea, it can be really useful when g77 goes weird on you. Oh, and the repository version of Ruuid doesn't require glib on OS X (sort of a heavy requirement for something like 5 typedefs), you might try building that version instead. On Oct 27, 2004, at 11:44 AM, Robert Gentleman wrote: > Hi, > First your real problem is that you do not have Ruuid installed (and > that is what graph reports as the problem). So that would be your > first port of call. There are some details of how to do this, and > what libraries you need in the mailing list archives. > > so do install.packages2("Ruuid") > and then see what libraries you do not have installed on your system, > then get them and install them. > > Second, you do not have g77, so you won't be able to install any > fortran code (and that is what is in hexbin). Again, this is because > you lack the right tools in OS X, so you need to find them and > install them. Stefano Iacus keeps a nice web page that describes what > you need to have installed etc. for building R packages. The OS X > FAQ, is another place to look for details (and probably the first > place to look), > > Best > Robert > > On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote: >> Using R v2.0.0 on MacOS X in the R console. >> I was able to install most of bioconductor. I wanted to use the >> GOstats >> package (amoung a few others), and it didn't install properly. So I >> went back to try to find the problem, and it seems that the graph >> package isn't installing. Any suggestions? >> Matt >> >>> getBioC("prog", develOK=T) >> Running getBioC version 1.2.66.... >> 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. >> >> Please select an installation directory: >> 1:/Users/mmccall/Library/R/library >> 2:/Library/Frameworks/R.framework/Resources/library >> Selection: 1 >> [1] "Attempting to download graph from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing graph" >> * Installing *source* package 'graph' ... >> ** libs >> gcc -no-cpp-precomp >> -I/Library/Frameworks/R.framework/Resources/include >> -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o >> graph.c: In function `intersectStrings': >> graph.c:39: warning: assignment makes pointer from integer without a >> cast >> graph.c:56: warning: assignment makes pointer from integer without a >> cast >> graph.c: In function `graphIntersection': >> graph.c:118: warning: assignment makes pointer from integer without a >> cast >> graph.c: In function `checkEdgeList': >> graph.c:157: warning: assignment makes pointer from integer without a >> cast >> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o >> graph.so graph.o -lcc_dynamic -framework R >> ld: warning multiple definitions of symbol _xerbla_ >> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of >> _xerbla_ >> ld: warning multiple definitions of symbol _crc32 >> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 >> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 >> ld: warning multiple definitions of symbol _get_crc_table >> /Library/Frameworks/R.framework/R(crc32.lo) definition of >> _get_crc_table >> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table >> ld: warning multiple definitions of symbol _deflate >> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate >> ld: warning multiple definitions of symbol _deflateCopy >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateCopy >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy >> ld: warning multiple definitions of symbol _deflateReset >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateReset >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset >> ld: warning multiple definitions of symbol _deflateSetDictionary >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateSetDictionary >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary >> ld: warning multiple definitions of symbol _deflateInit2_ >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateInit2_ >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ >> ld: warning multiple definitions of symbol _deflateEnd >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateEnd >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd >> ld: warning multiple definitions of symbol _deflateParams >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateParams >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams >> ld: warning multiple definitions of symbol _deflateInit_ >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateInit_ >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ >> ld: warning multiple definitions of symbol _zError >> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError >> /usr/lib/libz.1.dylib(zutil.o) definition of _zError >> ld: warning multiple definitions of symbol _zlibVersion >> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion >> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion >> ld: warning multiple definitions of symbol _inflateEnd >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateEnd >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd >> ld: warning multiple definitions of symbol _inflateSync >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSync >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync >> ld: warning multiple definitions of symbol _inflateSyncPoint >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSyncPoint >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint >> ld: warning multiple definitions of symbol _inflate >> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate >> ld: warning multiple definitions of symbol _inflateSetDictionary >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSetDictionary >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary >> ld: warning multiple definitions of symbol _inflateInit2_ >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateInit2_ >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ >> ld: warning multiple definitions of symbol _inflateReset >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateReset >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset >> ld: warning multiple definitions of symbol _inflateInit_ >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateInit_ >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ >> ld: warning multiple definitions of symbol _adler32 >> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 >> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 >> ld: warning multiple definitions of symbol _BC >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _BC >> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC >> ld: warning multiple definitions of symbol _UP >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _UP >> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP >> ld: warning multiple definitions of symbol _PC >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _PC >> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC >> ld: warning multiple definitions of symbol _gzeof >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof >> ld: warning multiple definitions of symbol _gzclose >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose >> ld: warning multiple definitions of symbol _gzdopen >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen >> ld: warning multiple definitions of symbol _gzerror >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror >> ld: warning multiple definitions of symbol _gzflush >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush >> ld: warning multiple definitions of symbol _gzgetc >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc >> ld: warning multiple definitions of symbol _gzgets >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets >> ld: warning multiple definitions of symbol _gzopen >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen >> ld: warning multiple definitions of symbol _gzprintf >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf >> ld: warning multiple definitions of symbol _gzputc >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc >> ld: warning multiple definitions of symbol _gzputs >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs >> ld: warning multiple definitions of symbol _gzread >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread >> ld: warning multiple definitions of symbol _gzrewind >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind >> ld: warning multiple definitions of symbol _gzseek >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek >> ld: warning multiple definitions of symbol _gzsetparams >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams >> ld: warning multiple definitions of symbol _gztell >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell >> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell >> ld: warning multiple definitions of symbol _gzwrite >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite >> ** R >> ** data >> ** inst >> ** save image >> [1] TRUE >> [1] TRUE >> [1] TRUE >> Loading required package: cluster >> Loading required package: Biobase >> Loading required package: tools >> Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >> [1] "propertyHolder" >> [1] "property" >> [1] "property" >> [1] "property<-" >> [1] "property<-" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "graph" >> [1] "edgemode" >> [1] "edgemode" >> [1] "edgemode<-" >> [1] "edgemode<-" >> [1] "graphNEL" >> [1] "initialize" >> [1] "nodes" >> [1] "nodes" >> [1] "nodes<-" >> [1] "nodes<-" >> [1] "edges" >> [1] "edges" >> [1] "edges" >> [1] "degree" >> [1] "degree" >> [1] "degree" >> [1] "edgeWeights" >> [1] "edgeWeights" >> [1] "adj" >> [1] "adj" >> [1] "acc" >> [1] "acc" >> [1] "DFS" >> [1] "DFS" >> [1] "edgeL" >> [1] "edgeL" >> [1] "subGraph" >> [1] "subGraph" >> [1] "intersection2" >> [1] "intersection2" >> [1] "intersection" >> [1] "intersection" >> [1] "join" >> [1] "join" >> [1] "union" >> [1] "union" >> [1] "complement" >> [1] "complement" >> [1] "connComp" >> [1] "connComp" >> [1] "isConnected" >> [1] "isConnected" >> [1] "numNodes" >> [1] "numNodes" >> [1] "numNodes" >> [1] "addNode" >> [1] "addNode" >> [1] "addNode" >> [1] "removeNode" >> [1] "removeNode" >> [1] "clearNode" >> [1] "clearNode" >> [1] "removeEdge" >> [1] "removeEdge" >> [1] "addEdge" >> [1] "addEdge" >> [1] "combineNodes" >> [1] "combineNodes" >> [1] "inEdges" >> [1] "inEdges" >> [1] "inEdges" >> [1] "inEdges" >> [1] "show" >> [1] "edgeNames" >> [1] "edgeNames" >> [1] "clusteringCoefficient" >> [1] "clusteringCoefficient" >> Error in assign("nullgraphID", getuuid()) : >> couldn't find function "getuuid" >> Execution halted >> cat: ** Removing '/Users/mmccall/Library/R/library/graph' >> ** Restoring previous '/Users/mmccall/Library/R/library/graph' >> stdout: Broken pipe >> ERROR: execution of package source for 'graph' failed >> [1] "Attempting to download hexbin from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing hexbin" >> * Installing *source* package 'hexbin' ... >> ** libs >> g77 -fno-common -g -O2 -c hbin.f -o hbin.o >> ** Removing '/Users/mmccall/Library/R/library/hexbin' >> make: g77: Command not found >> make: *** [hbin.o] Error 127 >> ERROR: compilation failed for package 'hexbin' >> ** Restoring previous '/Users/mmccall/Library/R/library/hexbin' >> [1] "Attempting to download Ruuid from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing Ruuid" >> * Installing *source* package 'Ruuid' ... >> creating cache ./config.cache >> checking for glib-config... no >> checking how to run the C preprocessor... cc -E >> checking for /usr/include/unistd.h... yes >> updating cache ./config.cache >> creating ./config.status >> creating src/Makevars >> ** libs >> gcc -no-cpp-precomp >> -I/Library/Frameworks/R.framework/Resources/include >> -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include >> -fno-common -g -O2 -c Rinit.c -o Rinit.o >> In file included from Ruuid.h:5, >> from Rinit.c:1: >> uuidP.h:24:18: glib.h: No such file or directory >> In file included from Ruuid.h:5, >> from Rinit.c:1: >> uuidP.h:36: error: parse error before "guint32" >> uuidP.h:36: warning: no semicolon at end of struct or union >> uuidP.h:37: warning: data definition has no type or storage class >> uuidP.h:38: error: parse error before "time_hi_and_version" >> uuidP.h:38: warning: data definition has no type or storage class >> uuidP.h:39: error: parse error before "clock_seq" >> uuidP.h:39: warning: data definition has no type or storage class >> uuidP.h:40: error: parse error before "node" >> uuidP.h:40: warning: data definition has no type or storage class >> uuidP.h:41: error: parse error before '}' token >> ** Removing '/Users/mmccall/Library/R/library/Ruuid' >> ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid' >> make: *** [Rinit.o] Error 1 >> ERROR: compilation failed for package 'Ruuid' >> From URL: >> http://www.bioconductor.org/repository/devel/package/Source >> graph version 1.4.22 >> hexbin version 1.1-2 >> Ruuid version 1.4.5 >> >> Packages Rgraphviz and rhdf5 require special libraries to be >> installed. >> Please see the URL http://www.bioconductor.org/faq.html#Other Notes >> for >> more details on installing these packages if they fail >> to install properly >> >> Warning messages: >> 1: Installation of package graph had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >> 2: Installation of package hexbin had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >> 3: Installation of package Ruuid had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --- > -----+ > | Robert Gentleman phone : (617) 632-5250 > | > | Associate Professor fax: (617) 632-2444 > | > | Department of Biostatistics office: M1B20 > | > | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu > | > +------------------------------------------------------------------- --- > -----+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --- Byron Ellis (ellis@stat.harvard.edu) "Oook" -- The Librarian