I am very confused by the R manual. According to the help pages, the system.file function may be used to find files relative to their installed path
> system.file("help", "AnIndex", package = "splines")
[1] "/Library/Frameworks/R.framework/Resources/library/splines/help/AnIndex"
Ok, so then I would expect that a file in my own package would also be obtainable using the same mechanism, but:
> library(reindeer)
> system.file("inst","default_parmeters.xlsx",package="reindeer",mustWork = TRUE)
Error in system.file("inst", "default_parmeters.xlsx", package = "reindeer", :
no file found
This hacky version works though:
> file.path(system.file(package="reindeer",mustWork = TRUE),"inst","default_parmeters.xlsx")
[1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/reindeer/inst/default_parmeters.xlsx"
I cannot see why? This behaviour seems very arbitrary to me right.
I am trying to run dada2 within RStudio. Normally I would run it in Windows. However because I want to run cutadapt as well I have had to create a Linux VM. With some help I now have dada2 and cutadapt installed on my VM. I have copied over my R code which works in RStudio in Windows. I have editted the code on my VM so that it points towards the correct directories, e.g. replaced "c:\Rtemp" with "~/Rtemp". I believe I have done this correctly as RStudio reads in dada2 and then my files just like it does when I start the script in RStudio in Windows. However I then get error messages that I don't get when I run the script in RStudio in windows.
fnFs <- sort(list.files(path, pattern="_R1_001.fastq", full.names = TRUE))
fnRs <- sort(list.files(path, pattern="_R2_001.fastq", full.names = TRUE))
sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)
plotQualityProfile(fnFs[1:2])
Error in (function (cond) :
error in evaluating the argument 'dirPath' in selecting a method for function 'qa': IncompatibleTypes
message: error in evaluating the argument 'x' in selecting a method for function 'which': error in evaluating the argument 'x' in selecting a method for function 'alphabetFrequency': invalid class “BStringSet” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
There are no "install" errors so I don't think the problem is missing installs. Is this error message indicating a problem with the amount of memory on my VM?
I recently ran into this problem while working through the dada2 tutorial.
I fixed it by loading up library(Biostrings) before loading dada2. I was under the impression that dada2 automatically loaded up Biostrings, but this was the fix. Hopefully it works for you.
I am attempting to use the plot() function in the biomod2 package, following a vignette here (http://finzi.psych.upenn.edu/usr/share/doc/library/biomod2/doc/Simple_species_modelling.pdf). Below is the error I am getting:
getwd()
# [1] "/home/gjanzen/Documents/Hufford/Drought/Data/Layers"
plot(myBiomodData)
Error in getExportedValue(pkg, name) : cannot open file
'~/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb': No
such file or directory In addition: Warning message: In
getExportedValue(pkg, name) : restarting interrupted promise
evaluation
I have confirmed that the Rdata.rdb exists, in the following directory:
f <- file.choose()
f
# [1] "/home/gjanzen/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb"
So, to me, it looks like the plot() function is looking in the wrong place. How can I change where this function looks for Rdata.rdb? Can I alter the path somehow? Or would changing my working directory fix this?
PS - This is my first post on Stack Overflow, so please forgive any mistakes in etiquette, and/or feel free to point them out to me so that I do not repeat them.
I think that the first thing to try is to reinstall the package viridisLite that seems to be the one that is causing troubles.
install.packages('viridisLite', dep = TRUE)
If this not solves the issue you should try to open a new plotting device threw x11() to check if the issue is not coming from the R (resp. RStudio) plotting device itself.
I have downloaded TreeTaggerv3.2 for Windows and have configured it per the install.txt. I am trying to use it in R with koRpus package. I have set the kRp.env as -
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en",
preset="en", treetagger="manual", format="file",
TT.tknz=TRUE, encoding="UTF-8" )
.My data to be tagged is in a file and trying to use it as treetag("myfile.txt") but it is throwing the error-
Error in matrix(unlist(strsplit(tagged.text, "\t")), ncol = 3, byrow = TRUE, :
'data' must be of a vector type, was 'NULL'
In addition: Warning message:
running command 'C:\windows\system32\cmd.exe /c C:\TreeTagger\bin\tag-english.bat
C:\Users\vivsingh\Desktop\NLP\tree_tag_ex.txt' had status 255
The standalone TreeTagger is working on by windows.Any idea on how it works?
I had the exact same error and warning while trying lemmatization on R word vector following Bernhard Learns blog using windows 7 and R 3.4.1 (x64). The issue was also appearing using textstem package but TreeTagger was running properly in cmd window.
I mixed several answers I found on this post and here is my steps and code running properly:
get into R win_library (~\Documents\R\win-library\3.4\rJava\jri\x64\jri.dll) and copy jri.dll (thanks kravi!) to replace it the parent folder.
close and restart R
library(koRpus)
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en", preset="en", treetagger="manual", format="file", TT.tknz=TRUE, encoding="UTF-8")
lemma_tagged <- treetag(lemma_unique$word_clean, treetagger="manual", format="obj", TT.tknz=FALSE , lang="en", TT.options=list(path="c:/TreeTagger", preset="en"))
lemma_tagged_tbl <- tbl_df(lemma_tagged#TT.res)
Hope it helps.
I am posting this answer to keep a record. I also faced the same issue due to incorrect specification of the location of jri.dll on 64-Bit processor and windows 8.1. If we call
set.kRp.env(TT.cmd="manual", lang="en", TT.options=list(path="/path/to/tree-tagger-windows-x.x/TreeTagger", preset="en")) and we follow either of following two steps, we can resolve this error:
While installing R, if we install only 64 Bit version of R, and
specify the proper path for these variables
LD_LIBRARY_PATH = /path/to/rJava/jri
JAVA_HOME = /path/to/jdk1.x.x
java.library.path = /path/to/rJava/jri/jri.dll
CLASSPATH = /path/to/rJava/jri
If we already installed both versions viz. 32 bit and 64 bit of R on your computer then just copy jri.dll from /path/to/rJava/jri/x64/jri.dll and replace at path/to/rJava/jri/jri.dll. Further, we need to set the path of above mentioned four variables.
I've got this issue (very similar I guess) and posted query to GitHub.
https://github.com/unDocUMeantIt/koRpus/issues/7
The current working solution for me for this case was easier than I could expect, just downgrading the koRpus package. This can change with time but this version should remain appropriate.
library("devtools")
install_github("unDocUMeantIt/koRpus", ref="0.06-5")
This package is not Java related they said.
You can face the same error while setting up the korpus environment and getting the result from treetagger. For example, when you use:
tagged.text <- treetag(
"C:/temp/sample_text.txt",
treetagger = "manual",
lang = "en",
TT.options = list(
path = "c:/Treetagger",
preset = "en"
),
doc_id = "sample"
)
You would receive a similar error
Error: Awww, this should not happen: TreeTagger didn't return any useful data.
This can happen if the local TreeTagger setup is incomplete or different from what presets expected.
You should re-run your command with the option 'debug=TRUE'. That will print all relevant configuration.
Look for a line starting with 'sys.tt.call:' and try to execute the full command following it in a command line terminal. Do not close this R session in the meantime, as 'debug=TRUE' will keep temporary files that might be needed.
If running the command after 'sys.tt.call:' does fail, you'll need to fix the TreeTagger setup.
If it does not fail but produce a table with proper results, please contact the author!
Here you need to change the value of treetagger, from
treetagger = "manual"
to
treetagger = "kRp.env"
However, before that remember to set the kRp.env as #Xochitl C. suggested in their answer
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en", preset="en", treetagger="manual", format="file", TT.tknz=TRUE, encoding="UTF-8")
Once you do this, you'll get the desired result.
As in What could cause a "bad magic number" error when loading an R workspace and how to avoid it? and R has magic number 'ëPNG' error, I'm getting a bad restore file magic number error:
> load("fossilien.dat")
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘fossilien.dat’ has magic number '"Samp'
Use of save versions prior to 2 is deprecated
Using the source function gives me a different error (similar to unexpected string constant):
> source("fossilien.dat")
Error in source("fossilien.dat") :
fossilien.dat:1:10: unexpected string constant
1: "Sample" "Sname"
^
This is especially frustrating as I'm confident the source of data is legit - its for a homework problem: ftp://stat.ethz.ch/Teaching/Datasets/WBL/fossilien.dat
None of the SO questions above were really answered properly so I thought I would try again.
Some details about my R installation:
> R.Version()
$platform
[1] "x86_64-apple-darwin9.8.0"
$version.string
[1] "R version 2.15.3 (2013-03-01)"
The read.table function ended up working: http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html
> fossildata <- read.table("fossilien.dat")
EDIT by CGW: load is for files in .rdata format, while your fossilien.dat clearly is an ASCII table. source executes the named file or object.