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Question: Cannot load bioconductor's packages installed
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gravatar for 郑淇
13.1 years ago by
郑淇10
郑淇10 wrote:
Good day, everone, I am a new user from China of Bioconductor and having some problems while using it at present. As I cannot find any related archives at FAQ documents of R and bioconductor, I have to turn to you for help. Maybe I should give you some information about my systerm and hardware first. I managed to get R and 'bioconductor' successfully installed on my personal computer, which is purchased from IBM company and whose operating systerm is 'Mandrake Linux' version 10.1. The version of R installed is 2.1.1, and that of bioconductor is the also the latest (must be version 1.7 as I get it installed following the 'bioconductor installation' procedure. Wish these were helpful in solving my problems. The biggest problem I have met is that I can not load the package "graph" that has already been installed. I downloaded it using "biocLite("graph") and the installation progress was certainly finished without errors or warnings, but it was werid that when I tried to load it by 'library("graph")', a mistake occurded and it died unexpectedly. The prompted messages is writed down below (with some words translated into English by myself due to my Chinese Version Operation Systerm): "> library("graph") error: assign("nullgraphID", getuuid()) : cannot find the function"getuuid" error: package'graph' writing and loading R failed error: loading 'graph' package/namespace failed." And these were all the packages I had loaded then: "> search() [1] ".GlobalEnv" "package:ALL" "package:cMAP" [4] "package:Ruuid" "package:cluster" "package:hgu133a" [7] "package:KEGG" "package:annotate" "package:GO" [10] "package:Biobase" "package:tools" "package:methods" [13] "package:stats" "package:graphics" "package:grDevices" [16] "package:utils" "package:datasets" "Autoloads" [19] "package:base" " This is the main problem I'd like to ask for help. Were there any obscurity in my description, please let me know and I will give extra information as much as possible. Eager to receive your reply! Bese wishes! Sincerely,yours Anonymous from China
ADD COMMENTlink modified 13.1 years ago by Seth Falcon7.4k • written 13.1 years ago by 郑淇10
0
gravatar for Seth Falcon
13.1 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi there, On 24 Oct 2005, zhengqi04 at mails.gucas.ac.cn wrote: > I am a new user from China of Bioconductor and having some problems > while using it at present. Welcome. I hope we will be able to help get you going. > The version of R installed is 2.1.1, and that of bioconductor > is the also the latest (must be version 1.7 as I get it installed > following the 'bioconductor installation' procedure. Wish these were > helpful in solving my problems. Actually, if you are using R 2.1.1, then biocLite will automatically install Bioc 1.6 (previous release) because that is the Bioconductor version compatible with R 2.1.1. For the most up to date code, use R 2.2.0 which will allow you to install Bioc 1.7 packages via the same biocLite method. > The biggest problem I have met is that I can not load the package > "graph" that has already been installed. I downloaded it using > "biocLite("graph") and the installation progress was certainly > finished without errors or warnings, Hmm, it should have installed the Ruuid package as a dependency. Are you sure it did not encounter an error installing Ruuid? > "> library("graph") > error: assign("nullgraphID", getuuid()) : > cannot find the function"getuuid" > error: package'graph' writing and loading R failed > error: loading 'graph' package/namespace failed." > > And these were all the packages I had loaded then: > "> search() > [1] ".GlobalEnv" "package:ALL" "package:cMAP" > [4] "package:Ruuid" "package:cluster" "package:hgu133a" > [7] "package:KEGG" "package:annotate" "package:GO" > [10] "package:Biobase" "package:tools" "package:methods" > [13] "package:stats" "package:graphics" "package:grDevices" > [16] "package:utils" "package:datasets" "Autoloads" > [19] "package:base" " The error message means that Ruuid was not found/functional. Here are a few things to try: 1. library(Ruuid) to test whether or not Ruuid is installed. 2. biocLite("Ruuid") 3. If Ruuid _is_ having installation problems, you may need to install some of the glib-devel rpm packages. The output from the installation should help. Best Wishes, + seth
ADD COMMENTlink written 13.1 years ago by Seth Falcon7.4k
0
gravatar for Li Long
13.1 years ago by
Li Long120
Li Long120 wrote:
Seems like you don't have "Ruuid" installed. Did you run biocLite("graph") only and nothing else? You can use "groupName" to install a subset of packages. Li > Good day, everone, > > I am a new user from China of Bioconductor and having some problems while > using it at present. As I cannot find any related archives at FAQ > documents of R and bioconductor, I have to turn to you for help. > Maybe I should give you some information about my systerm and hardware > first. I managed to get R and 'bioconductor' successfully installed on my > personal computer, which is purchased from IBM company and whose operating > systerm is 'Mandrake Linux' version 10.1. The version of R installed is > 2.1.1, and that of bioconductor is the also the latest (must be version > 1.7 as I get it installed following the 'bioconductor installation' > procedure. Wish these were helpful in solving my problems. > > The biggest problem I have met is that I can not load the package "graph" > that has already been installed. I downloaded it using "biocLite("graph") > and the installation progress was certainly finished without errors or > warnings, but it was werid that when I tried to load it by > 'library("graph")', a mistake occurded and it died unexpectedly. The > prompted messages is writed down below (with some words translated into > English by myself due to my Chinese Version Operation Systerm): > > "> library("graph") > error: assign("nullgraphID", getuuid()) : > cannot find the function"getuuid" > error: package'graph' writing and loading R failed > error: loading 'graph' package/namespace failed." > > And these were all the packages I had loaded then: > "> search() > [1] ".GlobalEnv" "package:ALL" "package:cMAP" > [4] "package:Ruuid" "package:cluster" "package:hgu133a" > [7] "package:KEGG" "package:annotate" "package:GO" > [10] "package:Biobase" "package:tools" "package:methods" > [13] "package:stats" "package:graphics" "package:grDevices" > [16] "package:utils" "package:datasets" "Autoloads" > [19] "package:base" " > > This is the main problem I'd like to ask for help. Were there any > obscurity in my description, please let me know and I will give extra > information as much as possible. > > Eager to receive your reply! > Bese wishes! > Sincerely,yours > Anonymous from China > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 13.1 years ago by Li Long120
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