Library not loaded: /usr/local/lib/libgvc.5.dylib (Rgraphviz)
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Peng Yu ▴ 940
@peng-yu-3586
Last seen 7.1 years ago
Hi, I have the following error. I only can find the following file. But I can't find libgvc.5.dylib on my system. Does anybody know what is wrong? ~$ ll -go /usr/local/lib/libgvc.6.dylib -rwxrwxr-x 1 988980 2012-05-21 00:21:09 /usr/local/lib/libgvc.6.dylib > library(Rgraphviz) Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: call: value[[3L]](cond) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgrap hviz/libs/x86_64/Rgraphviz.so': dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/libra ry/Rgraphviz/libs/x86_64/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgraph viz/libs/x86_64/Rgraphviz.so Reason: image not found Check that (1) graphviz is installed on your system; (2) the installed version of graphviz matches '2.26.3'; this is the version used to build this Rgraphviz package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin' directory is in the system 'PATH' variable. See additional instructions in the 'README' file of the Rgraphviz 'source' distribution, available at http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask further questions on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html Error: package/namespace load failed for ?Rgraphviz? -- Regards, Peng
Rgraphviz Rgraphviz • 1.5k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States
On Tue, Jul 17, 2012 at 6:10 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: > Hi, > > I have the following error. I only can find the following file. But I > can't find libgvc.5.dylib on my system. Does anybody know what is > wrong? > > ~$ ll -go /usr/local/lib/libgvc.6.dylib > -rwxrwxr-x 1 988980 2012-05-21 00:21:09 /usr/local/lib/libgvc.6.dylib > > >> library(Rgraphviz) > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > call: value[[3L]](cond) > error: unable to load shared object There is a README for the Rgraphviz package, available here: http://bioconductor.org/packages/release/bioc/readmes/Rgraphviz/README It says that you need to install graphviz first, preferably version 2.26.3, from here if you are running Snow Leopard or newer: http://www.graphviz.org/pub/graphviz/stable/macos/snowleopard/graphviz -2.26.3.pkg And from here if you are running Leopard: http://www.graphviz.org/pub/graphviz/stable/macos/leopard/graphviz-2.2 6.3.pkg Dan > '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgr aphviz/libs/x86_64/Rgraphviz.so': > dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/lib rary/Rgraphviz/libs/x86_64/Rgraphviz.so, > 6): Library not loaded: /usr/local/lib/libgvc.5.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgra phviz/libs/x86_64/Rgraphviz.so > Reason: image not found > > Check that (1) graphviz is installed on your system; (2) the > installed version of graphviz matches '2.26.3'; this is the version > used to build this Rgraphviz package; (3) graphviz is > accessible to R, e.g., the path to the graphviz 'bin' directory is > in the system 'PATH' variable. See additional instructions in the > 'README' file of the Rgraphviz 'source' > distribution, available at > > http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html > > Ask further questions on the Bioconductor mailing list > > http://bioconductor.org/docs/mailList.html > > > Error: package/namespace load failed for ?Rgraphviz? > > -- > Regards, > Peng > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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>> ~$ ll -go /usr/local/lib/libgvc.6.dylib >> -rwxrwxr-x 1 988980 2012-05-21 00:21:09 /usr/local/lib/libgvc.6.dylib Obviously, I have graphviz installed. Otherwise, I would not have the above file. The problem is that my installation is newer (see version below). ~$ dot -v dot - graphviz version 2.29.20120702.0446 (20120702.0446) libdir = "/opt/local/lib/graphviz" Activated plugin library: libgvplugin_pango.6.dylib Using textlayout: textlayout:cairo Activated plugin library: libgvplugin_dot_layout.6.dylib Using layout: dot:dot_layout Activated plugin library: libgvplugin_core.6.dylib Using render: dot:core Using device: dot:dot:core The plugin configuration file: /opt/local/lib/graphviz/config6 was successfully loaded. render : cairo dot eps fig gd lasi map pic pov ps quartz svg tk vml vrml xdot layout : circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi textlayout : textlayout device : bmp canon cgimage cmap cmapx cmapx_np dot eps exr fig gd gd2 gif gv imap imap_np ismap jp2 jpe jpeg jpg pct pdf pic pict plain plain-ext png pov ps ps2 psd sgi svg svgz tga tif tiff tk vml vmlz vrml wbmp webp x11 xdot xlib loadimage : (lib) bmp eps gd gd2 gif jpe jpeg jpg pdf png ps svg webp xbm > It says that you need to install graphviz first, preferably version > 2.26.3, from here if you are running Snow Leopard or newer: > http://www.graphviz.org/pub/graphviz/stable/macos/snowleopard/graphv iz-2.26.3.pkg Is there a maintainer who can build Rgraphviz for the latest graphviz? -- Regards, Peng
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On Tue, Jul 17, 2012 at 6:39 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>> ~$ ll -go /usr/local/lib/libgvc.6.dylib >>> -rwxrwxr-x 1 988980 2012-05-21 00:21:09 /usr/local/lib/libgvc.6.dylib > > Obviously, I have graphviz installed. Otherwise, I would not have the > above file. The problem is that my installation is newer (see version > below). > > ~$ dot -v > dot - graphviz version 2.29.20120702.0446 (20120702.0446) > libdir = "/opt/local/lib/graphviz" > Activated plugin library: libgvplugin_pango.6.dylib > Using textlayout: textlayout:cairo > Activated plugin library: libgvplugin_dot_layout.6.dylib > Using layout: dot:dot_layout > Activated plugin library: libgvplugin_core.6.dylib > Using render: dot:core > Using device: dot:dot:core > The plugin configuration file: > /opt/local/lib/graphviz/config6 > was successfully loaded. > render : cairo dot eps fig gd lasi map pic pov ps quartz svg tk > vml vrml xdot > layout : circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi > textlayout : textlayout > device : bmp canon cgimage cmap cmapx cmapx_np dot eps exr fig gd > gd2 gif gv imap imap_np ismap jp2 jpe jpeg jpg pct pdf pic pict plain > plain-ext png pov ps ps2 psd sgi svg svgz tga tif tiff tk vml vmlz > vrml wbmp webp x11 xdot xlib > loadimage : (lib) bmp eps gd gd2 gif jpe jpeg jpg pdf png ps svg webp xbm > > >> It says that you need to install graphviz first, preferably version >> 2.26.3, from here if you are running Snow Leopard or newer: > >> http://www.graphviz.org/pub/graphviz/stable/macos/snowleopard/graph viz-2.26.3.pkg > > Is there a maintainer who can build Rgraphviz for the latest graphviz? There is a version of graphviz in the works that has graphviz bundled, so you won't need to worry about installing graphviz at all. In the meantime, installing the suggested version usually works. Dan > > -- > Regards, > Peng
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