Thank you, Vincent. It installed Ruuid from the command line. Earlier, I was trying to install Ruuid using R Gui and it doesn't work. Thanks a lot. Neel On Mar 3, 2011, at 6:40 AM, Vincent Carey wrote: > if you used fink, glib-config should be in /sw/bin -- check. then > make sure /sw/bin is in your PATH > > in a terminal > > echo $PATH > > if you do not see :/sw/bin: somewhere in the result, you must do > > export PATH=$PATH:/sw/bin > > then > > which glib-config > > should have a response /sw/bin/glib-config > > in the same session, attempt the Ruuid installation from source > > you can change your shell initialization to include the export PATH > above, typically $HOME/.bashrc is where that will be stored > > On Thu, Mar 3, 2011 at 12:45 AM, Neel Aluru <naluru at="" whoi.edu=""> wrote: >> Hi Vincent, >> >> Thanks for the following guidelines. I followed the instructions and I still have the problem. I restarted the computer after installing Fink. >> >> Any help is appreciated. >> >> Thank you, >> >> Neel >> >> Here is what I get: >> >>> source("http://bioconductor.org/biocLite.R") >> BioC_mirror = http://www.bioconductor.org >> Change using chooseBioCmirror(). >>> biocLite("Ruuid", type="source") >> Using R version 2.12.1, biocinstall version 2.7.4. >> Installing Bioconductor version 2.7 packages: >> [1] "Ruuid" >> Please wait... >> >> Installing package(s) into ?/Users/naluru/Library/R/2.12/library? >> (as ?lib? is unspecified) >> trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contr ib/Ruuid_1.28.0.tar.gz' >> Content type 'application/x-gzip' length 71906 bytes (70 Kb) >> opened URL >> ================================================== >> downloaded 70 Kb >> >> * installing *source* package ?Ruuid? ... >> checking for pkg-config... no >> checking for glib-config... no >> configure: error: No glib package information found >> ERROR: configuration failed for package ?Ruuid? >> * removing ?/Users/naluru/Library/R/2.12/library/Ruuid? >> >> The downloaded packages are in >> ?/private/var/folders/DF/DFRfPr1YEfih-Ckx- GdJAk+++TI/-Tmp-/Rtmp7PzZPu/downloaded_packages? >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'Ruuid' had non-zero exit status >>> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.12.1 >> >> I checked if I have the glib package is installed in my computer and here are the different glib packages installed from Fink. >> >> >> naluru$ fink list >> >> i glib 1.2.10-51 Common C routines used by Gtk+ and other ... >> glib-pm5100 1.222-1 Glib:: perl module (bindings for glib2) >> glib-pm588 1.222-1 Glib:: perl module (bindings for glib2) >> i glib-shlibs 1.2.10-51 Common C routines used by Gtk+ and other ... >> i glib2-dev 2.22.4-4 Handy library of utility functions >> i glib2-shlibs 2.22.4-4 Handy library of utility functions >> glibmm2.4 2.22.2-1 C++ interface for the glib2 library >> glibmm2.4-dev 2.22.2-1 C++ interface for the glib2 library >> glibmm2.4-shlib 2.22.2-1 C++ interface for the glib2 library >> >> On Feb 26, 2011, at 7:10 AM, Vincent Carey wrote: >> >>> This problem was addressed on Feb 7. Let us know if the solution does >>> not work for you. The problem concerns a dependency of Ruuid >>> infrastructure on glib2, which is not uniformly available on MacOSX >>> machines. Quoting below from the Feb 7 exchange >>> >>> Dear Vincent, >>> >>> Thanks a lot. I have got GGtools installed in my Mac book pro (with >>> updated Mac OS and Xcode). >>> >>> What I have done: >>> (1). install fink in order to let all unix program run in Mac, >>> following the manual in fink website (http://www.finkproject.org/). >>> >>> (2). then, run "sudo fink install glib glib2-dev". >>> >>> (3). next, log in R, and >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("Ruuid", type="source") # you must install Ruuid from source. >>> biocLite("GGtools") >>> >>> (4). invoke GGtools >>> library(GGtools) >>> >>> I need to mention that all my progresses were got under helps of Mr. >>> Vincent and Martin, especially Vincent has given me much. >>> >>> Thanks a lot. >>> >>> Best, >>> >>> On Sat, Feb 26, 2011 at 6:42 AM, Neel Aluru <naluru at="" whoi.edu=""> wrote: >>>> Hello, >>>> >>>> I have installed GGtools and GGBase and when I try to load them, I keep getting the following error messages. I really appreciate if someone can help me in sorting this problem. >>>> >>>> Thank you, >>>> Neel >>>> >>>> >>>> [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0] >>>> >>>> [Workspace restored from /Users/naluru/.RData] >>>> [History restored from /Users/naluru/.Rapp.history] >>>> >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material. To view, type >>>> 'openVignette()'. To cite Bioconductor, see >>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>> Loading required package: snpMatrix >>>> Loading required package: survival >>>> Loading required package: splines >>>> Loading required package: RSQLite >>>> Loading required package: DBI >>>> Error in as.environment(pos) : >>>> no item called "newtable" on the search list >>>> In addition: Warning message: >>>> In objects(newtable, all.names = TRUE) : >>>> ?newtable? converted to character string >>>> Error: package/namespace load failed for 'GGBase' >>>> Loading required package: GGBase >>>> Error in as.environment(pos) : >>>> no item called "newtable" on the search list >>>> In addition: Warning message: >>>> In objects(newtable, all.names = TRUE) : >>>> ?newtable? converted to character string >>>> Error: package 'GGBase' could not be loaded >>>> >>>>> sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] splines stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] RSQLite_0.9-4 DBI_0.2-5 snpMatrix_1.14.1 survival_2.36-2 Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.28.0 AnnotationDbi_1.12.0 graph_1.28.0 GSEABase_1.12.2 tools_2.12.1 >>>> [6] XML_3.2-0 xtable_1.5-6 >>>>> >>>> >>>> >>>> Neel Aluru >>>> Visiting Investigator >>>> Biology Department >>>> Redfield Building 3-04 >>>> Woods Hole Oceanographic Institution >>>> 45, Water Street >>>> Woods Hole, MA >>>> >>>> naluru at whoi.edu >>>> 508-289-3607 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >> >> Neel Aluru >> Visiting Investigator >> Biology Department >> Redfield Building 3-04 >> Woods Hole Oceanographic Institution >> 45, Water Street >> Woods Hole, MA >> >> naluru at whoi.edu >> 508-289-3607 >> >> > Neel Aluru Visiting Investigator Biology Department Redfield Building 3-04 Woods Hole Oceanographic Institution 45, Water Street Woods Hole, MA naluru at whoi.edu 508-289-3607