Displaying 20 results from an estimated 35 matches for "openvignett".
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openvignette
2004 Jan 22
1
File permissions and packages, openVignette
...rwxr--
o Files - -rw-r--r--
Everything builds and runs through 'R CMD check' fine with no warnings
or errors...
I now install the package as root, and again it goes in fine - and I can
see the library, its functions, and their man pages, when I fire up R.
However, when I call openVignette(), my package vignette is not visible.
Going into the file system, finding the installed library, and doing
'chmod -R 777 *' on the package, seems to fix the problem, without
breaking anything else.
However, I suspect I'm not supposed to do this! :-) Can anyone tell me
what permissio...
2005 Oct 19
2
Error in opening .RData containing a genefilter object
...blem?
Below is a short r session to reproduce the error:
...
[Previously saved workspace restored]
> library(genefilter)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: survival
Loading required package: splines
> f1 <- kOverA(5, 60)
> q()
Save workspace image? [y/n/c]: y
[computer:admin]$ r
R : Copyright 2005, The R Foundation for Statist...
2005 Mar 15
1
How do I call a masked function in a package without a namespace?
...d package: cluster
Loading required package: Ruuid
Creating a new generic function for "print" in "Ruuid"
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
> conflicts()
[1] "last.warning" "degree" "body<-" "print" "split"
[6] "union"
> sna::degree()
Error in loadNamespace(nam...
2008 Nov 15
1
unable to view vignette in R
...:
ISSUE:
Cannot view R vignettes due in Ubuntu Linux (a debian variant).
note: this issue has been posted to this list before with no responses given
see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html
DETAILS:
I am trying to view an R vignette.
Here is the situation: I issue the openvignette(), then select the
vignette I wish to view...and the system returns:
"Could not get a file descriptor referring to the console."
This action should spawn a ps viewer displaying the contents of the
vignette for my enjoyment.
I suspect it may have something to do with the call to the p...
2007 Mar 05
1
Error loading a dependency in a package: missing namespace?
...es ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... ERROR
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: outliers
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
= keep.source) :
in 'pcrAnalysis' classes for export not defi...
2010 Jul 06
1
Error in affypdnn package
...ex for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error-
> library(affypdnn)
Loading required package: affy
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)'.
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
> library(hgu133atagprobe)
Loading required package...
2009 Dec 14
2
Error with hgu133a2.db
...b'
> utils:::menuInstallLocal()
package 'hgu133a2.db' successfully unpacked and MD5 sums checked
> library(hgu133a2.db)
Loading required package: AnnotationDbi
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: DBI
Error in fun(...) : could not find function "createAnnObjs.HUMANCHIP_DB"
In addition: Warning message:
package 'hgu133a2.db' was...
2010 Aug 27
1
Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'
...ked and MD5 sums
checked"
But when I am trying to load this library I get an error:
> library(IlluminaHumanMethylation27k.db)
Loading required package: AnnotationDbi
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: org.Hs.eg.db
Loading required package: DBI
Error : .onLoad failed in loadNamespace() for
'IlluminaHumanMethylation27k.db', details:
call: s...
2005 Aug 31
1
Bioconductor and R-devel
...ron.
When I ran qc assessment on Affymetrix latin square data set, I got the
following output,
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: reposTools
Welcome to 'simpleaffy' V 2.1.3
Produced by The Paterson Institute for Cancer Research
and funded by CANCER RESEARCH UK....
2005 May 02
2
"Special" characters in URI
...lso be a problem with others i.e. reserved characters
in URI syntax.
My R example is:
R> library("annotate")
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
R> library(XML)
R> tmp$term <- "gorjanc g[au]"
R> tmp$URL <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?term=gorjanc g[au]"
R> tmp
$term
[1] "gorjanc g[...
2005 Mar 15
0
How do I call a masked function in a package without a na mespace?
...e: Ruuid
> : Creating a new generic function for "print" in "Ruuid"
> : Loading required package: Biobase
> : Loading required package: tools
> : Welcome to Bioconductor
> : Vignettes contain introductory material. To view,
> : simply type: openVignette()
> : For details on reading vignettes, see
> : the openVignette help page.
> : > conflicts()
> : [1] "last.warning" "degree" "body<-" "print"
> "split"
> : [6] "union"
>...
2006 Nov 11
1
Install bioconductor
...all_locations.o mas5calls.o
qnorm.o rma2.o rma_background2.o rma_common.o -L/usr/lib/R/lib -lR
** R
** data
** demo
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affyio
Error: package 'affyio' could not be loaded
In addition: Warning message:
there is no package called 'affyio' in: library(pkg, chara...
2006 Oct 12
1
getMethods() not finding all methods
...p my way through the source. Is there another
way to get all methods that I should be using?
Any info appreciated.
> library(affy)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affyio
> getMethods("geneNames")
An object of class ?MethodsList?
Slot "methods":
$ExpressionSet
Method Definition:
function (objec...
2008 Apr 26
2
3 questions: debug R script, multi-level sorts, and multi-gsub
Hi,
1) I ran a script say test.R. It ran and terminated with an error. However,
I am not sure where the error occur.
> source("test.R")
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Error: subscript out of bounds
2) I have looked deeply into R, but can't fine multi-level sorts.
3) I have a vector of words, several of which need to be replaced by
diffe...
2010 Jul 06
2
Could not find createData function
...w to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(affy)
Loading required package: Biobase
Welcome to Bioconductor
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
> library(maanova)
Attaching package: 'maanova'
The following object(s) are masked from 'package:base':
norm
> abf1.raw <- read.madata("g...
2006 Aug 11
1
[BioC] problem loading affycoretools (more details)
...terface to help.
>Type 'q()' to quit R.
>
>Loading required package: affy
>Loading required package: Biobase
>Loading required package: tools
>
>Welcome to Bioconductor
>
>
> Vignettes contain introductory material.
>
> To view, simply type 'openVignette()' or start with 'help(Biobase)'.
>
> For details on reading vignettes, see the openVignette help page.
>
>
>Loading required package: affyio
>Loading required package: affydata
>Loading required package: Biobase
>Loading required package: gcrma
>Loading...
2009 Dec 28
2
[BioC] make.cdf.package: Error: cannot allocate vector of size 1 Kb
..._0-st-v1.text.cdf.zip
>>
>> $ Rscript MoEx-1_0-st-v1.cdf.R
>>>
>>> library(makecdfenv)
>>
>> 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: affy
>> Loading required package: affyio
>>>
>>> sessionInfo()
>>
>> R version 2.10.0 (2...
2007 Sep 25
1
'load' does not properly add 'show' methods for classes extending 'list'
...#39;show' method is not added to the appropriate
method table.
> load("/tmp/x.Rda")
> x
Loading required package: GSEABase
Loading required package: Biobase
Loading required package: tools
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: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
An object of class "GeneSetCollection"
[[1]]
setName: NA
gen...
2010 Feb 08
1
objects masked from packages
...packages. one of them is affyPLM, which
also have a S3 class named preprocess.
Each time I'm using the program i get the message:
> library(affyPLM)
Lade nötiges Paket: affy
Lade nötiges Paket: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Lade nötiges Paket: gcrma
Lade nötiges Paket: preprocessCore
Attache Paket: 'affyPLM'
The following object(s) are masked from package:affyAnalysis :
prepr...
2009 Sep 10
1
importing/loading package without a namespace
...age subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
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: qcc
Error : package 'qcc' does not have a name space
Error: package/namespace load failed for 'nvQC'
Execution halted
It looks like...