I want to use the function "makeTxDbfromGFF", which is part of the GenomicFeatures package. This function used to work perfectly until now, I get the following output:
makeTxDbFromGFF("/file/to/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf")
>Import genomic features from the file as a GRanges object ... OK
>Prepare the 'metadata' data frame ... OK
>Make the TxDb object ... Error in c(x, value) :
could not find symbol "recursive" in environment of the generic function
This function works on my Mac, but not on my Linux workstation. Here some details to my session:
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
I already uninstalled the new version 1.26.3 and installed the previous version (1.24.5), but I get the same error. On my Mac I use the version 1.26.2.
My research so far was not very successful. I just found out it might be due to some inconsistency with other software/packages(?).
Related
I am trying to write a reproducible R script so whenever I run the code I will get the results without any issue once the code is completed. Therefore, I am saving version of packages used in the code into a separate folder using the checkpoint package in R. The code I am using is as follows.
library(checkpoint)
create_checkpoint(snapshot_date = "2022-03-14", r_version = "4.0.4",
checkpoint_location = "E:/My Projects/Documents/GeriatricsCohorting_Project_Checkpoint")
This works on my personal laptop but doesn't work on a remote desktop. I get the following error:
Creating checkpoint directory C:/Users/e22336/Documents/.checkpoint/2022-03-14/lib/x86_64-w64-mingw32/4.0.4
Error in x[] <- if (!is.list(x)) x else if (inherits(x, "condition")) "<error>" else if
(is.recursive(x)) lapply(x,: object of type 'environment' is not subsettable
I am not sure where I make error. Any help is appreciated. Thanks in advance!
EDIT: The session info and R version is as follows:
sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
packageVersion("checkpoint")
‘1.0.0’
I am new to R-programming and I am trying to install Slidify and I am currently having a problem. I am running on the below version of RStudio:
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
I am using the below code to install Slidify:
install_github("slidify", "ramnathv")
install_github("slidifyLibraries", "ramnathv")*
I get the following error:
'C:\Program' is not recognized as an internal or external command, operable program or batch file.
Error: Command failed (1)
In addition: Warning message:
Username parameter is deprecated. Please use ramnathv/slidifyLibraries
I have also tried the below code to install Slidify:
pkgs <- c('ramnathv/slidifyLibraries', 'ramnathv/slidify')
devtools::install_github(pkgs)*
and I get the following error:
Error: Command failed (1)
Does anyone have experience installing Slidify?
1) install_github() function is in devtools package, so first you have to install this package using install.packages("devtools").
2) Then load the library using
library(devtools)
3) Now use your code
install_github("slidify", "ramnathv")
install_github("slidifyLibraries", "ramnathv")
It will work properly.
I'm having a similar problem as this one:
RODBC and Access - Loading data
but I'm working on Ubuntu 14.04 OS.
As stated, I need to query an Access file I have. I've tried
db <- "foo.accdb"
con <- odbcConnect(db)
which obviously doesn't work as the function I should use is odbcConnectAccess2007(), which is not available for package RODBC and is not listed on the manual:
http://cran.r-project.org/web/packages/RODBC/RODBC.pdf
I'm using RStudio Version 0.98.1091 with
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
My question is:
Is there any way I can access an Access database in a file using R from an Ubuntu computer?
In RStudio,
help.search('slider')
Returns this error:
Error in vignette_type(Outfile) : Vignette product ‘NA’ does not have a known filename extension (‘NA’)
However:
Other searches (such as help.search('ARMA')) appear to be working correctly in RStudio.
Running help.search('slider')in the R for Mac OS X GUI works as expected.
Any ideas what the problem might be?
Setup:
MBP OS X Version 10.9.4
RStudio Version 0.98.978
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
I'm getting a strange error when loading .Rdata produced on one OS and transferred to another. On a Windows machine I generate a large number of plots and store them in a .Rdata file. I then transfer them to a linux server running CentOS 5 and access them by loading the file and recalling the plot.
When I run the following lines on CentOS I get an error:
library(ggplot2)
load('mydata.Rdata')
p
Error in UseMethod("facet_train_layout") :
no applicable method for 'facet_train_layout' applied to an object of class "c('proto', 'environment')"
The Windows 7 OS that was used to produce this .Rdata file is using the following version of R:
R version 2.14.2 (2012-02-29) Copyright (C) 2012 The R Foundation for
Statistical Computing ISBN 3-900051-07-0 Platform:
x86_64-pc-mingw32/x64 (64-bit)
The CentOS system that produces an error is as follows:
R version 2.14.2 (2012-02-29) Copyright (C) 2012 The R Foundation for
Statistical Computing ISBN 3-900051-07-0 Platform: i686-pc-linux-gnu
(32-bit)
The ggplot2 version on both systems is ggplot2_0.9.2.1. This process has worked fine for the last six months, the only problem has been today due to an update and I don't understand what is going wrong.
Both versions of R were upgraded to 2.14.2, as well as the ggplot package to ggplot2_0.9.2.1.
I presume the old version was 0.8.9 or below. There was a fundamental change with version 0.9.0:
FACETS
Converted from proto to S3 objects, and class methods (somewhat) documented in facet.r. This should make it easier to develop new
types of facetting specifications.
See http://cran.r-project.org/web/packages/ggplot2/NEWS for more information