RBGL function highlyConnSG not recognized
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burak kutlu ▴ 200
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Tony Chiang ▴ 570
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Burak, you will get better answers if you provide a complete set of commands that, starting from a fresh R session, lead to your error. You didn't tell us what net1 is nor which expressions you have evaluated before. If you expect others to guess, they may not be able or willing to do it. Best wishes Wolfgang Tony Chiang ha scritto: > Hi Burak, > > First thing to do is to update your R and RBGL. The current released version > is 2.6 though the latest is a patched version (someone will correct me if I > am wrong). If the trouble still persists, let us know. > > Cheers, > --Tony > > On Dec 19, 2007 9:17 AM, burak kutlu <burak_kutlu at="" yahoo.com=""> wrote: > >> Hi >> I am trying to understand why 'highlyConnSG' does not work for me. Other >> RBGL functions seem to work fine. >> Error message and sessionInfo is below, any ideas? >> Thanks a lot >> -burak >> >> >>> highlyConnSG(net1) >> Error: could not find function "highlyConnSG" >>> >>> sessionInfo() >> R version 2.5.0 (2007-04-23) >> i686-pc-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >> [7] "base" >> >> other attached packages: >> gaggle rJava RBGL graph >> "1.4.0" "0.4-16" "1.3.13" "1.14.2" >> >> >> >> >> >> >> __________________________________________________________________ __________________ >> Looking for last minute shopping deals? >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, burak kutlu wrote: > Hi Wolfang > > Thanks for the warning: I am trying to be a better BioC poster every day! > I thought that the function error I am getting is independent of the graphNEL object, > which I should not have assumed?? > > The error message that I am getting is the same for all types of networks. > As an example, I have used a sample network that comes with the 'RBGL' package. > The commands and the sessionInfo is below. All this was done on a Linux Box. > > In the meantime, I have used an up-to-date version of R and RBCF package on my Windows machine > and I get the same error with the identical commands. The example is the same for my linux machine. Error and sessionInfo is below. > > Thanks again. > -burak > > ####### Begin: Commands and SessionInfo() Windows machine ########## > >> library(graph) >> utils:::menuInstallLocal() > package 'XML' successfully unpacked and MD5 sums checked > package 'RBGL' successfully unpacked and MD5 sums checked > updating HTML package descriptions So, now why are you installing these packages and why from local zip files? The advice given very often here is to use biocLite for all installing, please use it. But most importantly, there is no reason to reinstall these (your previous posts suggest that you have already installed them). And you seem to be very confused about the difference between installing (which you do once) and loading, which you do often. I suspect that all you want here is library(XML) library(RBGL) >> net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL"))) >> >> net1 > A graphNEL graph with directed edges > Number of Nodes = 4 > Number of Edges = 3 >> highlyConnSG(net1) > Error: could not find function "highlyConnSG" >> sessionInfo() > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] graph_1.16.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 tools_2.6.1 XML_1.9-0 > well - since you did not load the RBGL package it is not there and R cannot find the functions. use library(RBGL) > > > ####### End: Commands and SessionInfo() Windows machine ########## > > > > ####### Begin: Commands and SessionInfo() Linux machine ########## > >> library(RBGL) > Loading required package: graph >> net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL"))) > Loading required package: XML > > Attaching package: 'XML' > > > The following object(s) are masked from package:graph : > > addNode > >> net1 > A graphNEL graph with directed edges > Number of Nodes = 4 > Number of Edges = 3 >> highlyConnSG(net1) > Error: could not find function "highlyConnSG" >> sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > other attached packages: > XML RBGL graph > "1.9-0" "1.3.13" "1.14.2" > > > ####### End: Commands and SessionInfo() Linux machine ########## > > > > > > > Burak, > > you will get better answers if you provide a complete set of commands > that, starting from a fresh R session, lead to your error. You didn't > tell us what net1 is nor which expressions you have evaluated before. If > you expect others to guess, they may not be able or willing to do it. > > Best wishes > Wolfgang > > Tony Chiang ha scritto: >> Hi Burak, >> >> First thing to do is to update your R and RBGL. The current released version >> is 2.6 though the latest is a patched version (someone will correct me if I >> am wrong). If the trouble still persists, let us know. >> >> Cheers, >> --Tony >> >> On Dec 19, 2007 9:17 AM, burak kutlu <burak_kutlu at="" ...=""> wrote: >> >>> Hi >>> I am trying to understand why 'highlyConnSG' does not work for me. Other >>> RBGL functions seem to work fine. >>> Error message and sessionInfo is below, any ideas? >>> Thanks a lot >>> -burak >>> >>> >>>> highlyConnSG(net1) >>> Error: could not find function "highlyConnSG" >>>> sessionInfo() >>> R version 2.5.0 (2007-04-23) >>> i686-pc-linux-gnu >>> >>> locale: >>> >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >>> [7] "base" >>> >>> other attached packages: >>> gaggle rJava RBGL graph >>> "1.4.0" "0.4-16" "1.3.13" "1.14.2" >>> > > > > ______________________________________________________________ ______________________ > Looking for last minute shopping deals? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Dear Burak, to supplement what Robert said, please check http://www.stats.bris.ac.uk/R/doc/manuals/R-intro.html and particular Chapter 13 "Packages". Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Robert Gentleman wrote: > Hi, > > burak kutlu wrote: >> Hi Wolfang >> >> Thanks for the warning: I am trying to be a better BioC poster every day! >> I thought that the function error I am getting is independent of the graphNEL object, >> which I should not have assumed?? >> >> The error message that I am getting is the same for all types of networks. >> As an example, I have used a sample network that comes with the 'RBGL' package. >> The commands and the sessionInfo is below. All this was done on a Linux Box. >> >> In the meantime, I have used an up-to-date version of R and RBCF package on my Windows machine >> and I get the same error with the identical commands. The example is the same for my linux machine. Error and sessionInfo is below. >> >> Thanks again. >> -burak >> >> ####### Begin: Commands and SessionInfo() Windows machine ########## >> >>> library(graph) >>> utils:::menuInstallLocal() >> package 'XML' successfully unpacked and MD5 sums checked >> package 'RBGL' successfully unpacked and MD5 sums checked >> updating HTML package descriptions > > So, now why are you installing these packages and why from local zip > files? The advice given very often here is to use biocLite for all > installing, please use it. But most importantly, there is no reason to > reinstall these (your previous posts suggest that you have already > installed them). And you seem to be very confused about the difference > between installing (which you do once) and loading, which you do often. > > I suspect that all you want here is > > library(XML) > library(RBGL) > > >>> net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL"))) >>> >>> net1 >> A graphNEL graph with directed edges >> Number of Nodes = 4 >> Number of Edges = 3 >>> highlyConnSG(net1) >> Error: could not find function "highlyConnSG" >>> sessionInfo() >> R version 2.6.1 (2007-11-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] graph_1.16.1 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.9 tools_2.6.1 XML_1.9-0 >> > > well - since you did not load the RBGL package it is not there > and R cannot find the functions. > > use > library(RBGL) > >> >> ####### End: Commands and SessionInfo() Windows machine ########## >> >> >> >> ####### Begin: Commands and SessionInfo() Linux machine ########## >> >>> library(RBGL) >> Loading required package: graph >>> net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL"))) >> Loading required package: XML >> >> Attaching package: 'XML' >> >> >> The following object(s) are masked from package:graph : >> >> addNode >> >>> net1 >> A graphNEL graph with directed edges >> Number of Nodes = 4 >> Number of Edges = 3 >>> highlyConnSG(net1) >> Error: could not find function "highlyConnSG" >>> sessionInfo() >> R version 2.5.0 (2007-04-23) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >> [7] "base" >> >> other attached packages: >> XML RBGL graph >> "1.9-0" "1.3.13" "1.14.2" >> >> >> ####### End: Commands and SessionInfo() Linux machine ########## >> >> >> >> >> >> >> Burak, >> >> you will get better answers if you provide a complete set of commands >> that, starting from a fresh R session, lead to your error. You didn't >> tell us what net1 is nor which expressions you have evaluated before. If >> you expect others to guess, they may not be able or willing to do it. >> >> Best wishes >> Wolfgang >> >> Tony Chiang ha scritto: >>> Hi Burak, >>> >>> First thing to do is to update your R and RBGL. The current released version >>> is 2.6 though the latest is a patched version (someone will correct me if I >>> am wrong). If the trouble still persists, let us know. >>> >>> Cheers, >>> --Tony >>> >>> On Dec 19, 2007 9:17 AM, burak kutlu <burak_kutlu at="" ...=""> wrote: >>> >>>> Hi >>>> I am trying to understand why 'highlyConnSG' does not work for me. Other >>>> RBGL functions seem to work fine. >>>> Error message and sessionInfo is below, any ideas? >>>> Thanks a lot >>>> -burak >>>> >>>> >>>>> highlyConnSG(net1) >>>> Error: could not find function "highlyConnSG" >>>>> sessionInfo() >>>> R version 2.5.0 (2007-04-23) >>>> i686-pc-linux-gnu >>>> >>>> locale: >>>> >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=e n_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US. UTF-8;LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >>>> [7] "base" >>>> >>>> other attached packages: >>>> gaggle rJava RBGL graph >>>> "1.4.0" "0.4-16" "1.3.13" "1.14.2"
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