Question: GGtools and GGBase installation problems
0
gravatar for Neel Aluru
8.8 years ago by
Neel Aluru450
United States
Neel Aluru450 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/contrib/ 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
ADD COMMENTlink modified 8.8 years ago by Vincent J. Carey, Jr.6.3k • written 8.8 years ago by Neel Aluru450
Answer: GGtools and GGBase installation problems
0
gravatar for Vincent J. Carey, Jr.
8.8 years ago by
United States
Vincent J. Carey, Jr.6.3k 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/contri b/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 > >
ADD COMMENTlink written 8.8 years ago by Vincent J. Carey, Jr.6.3k
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
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