Problem installing graph package
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Matt McCall ▴ 50
@matt-mccall-926
Last seen 7.2 years ago
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) >
Ruuid rhdf5 graph hexbin Rgraphviz Ruuid rhdf5 graph hexbin Rgraphviz • 1.1k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 6.6 years ago
United States
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 | +--------------------------------------------------------------------- ------+
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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
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