I have read this question and answer here Read multiple .gpx files on reading GPX files in R. At the end of the question, the question setter notes "To run readGPS you will need the open source GPSBabel program installed and referenced in your PATH variable."
I have installed GPSBabel, but am unsure how to link it to R so that the supplied code works.
library(maptools)
gpx.raw <- readGPS(i = "gpx", f = "Data/Waypoints_11-MAY-18.gpx", type="w")
Running the code at the head of the question (above) with my own filename returns the error
Error in readGPS(i = "gpx", f = "Data/Waypoints_11-MAY-18.gpx", type = "w") :
gpsbabel not found
I had this problem, and I downloaded and installed GPSBabel, copied of the path for where it installed, and then:
setwd("C:/Program Files (x86)/GPSBabel")
That took care of it for me, not sure if there is a simpler way to do this.
Related
I have long-read RNA sequencing data from PacBio IsoSeq and trying to use IsoPops software (https://kellycochran.github.io/IsoPops/site_files/walkthrough.html) to generate graphs to interpret the data. I am new to R-studio so have limited proficiency. There is a walkthrough for the program which seems quite intuitive. I have successsfully installed the package on R Studio, and have opened the library and assigned variables to the files I have (which include a fasta file, gff file and abundance files). Once I've successfully assigned variables to the files, I'm supposed to generate a rawdb using the function compile_raw_db. However, when I do this function I get the error:
Error in system(command = paste("head -n1 ", filename, step = ""), intern = T) :
'head' not found
I've used the head -n1 function in linux command line, and can see that there definitely is a header and contents in the file. The error occurs for any file that I give to R studio, so my reasoning is that the programme is not recognizing the files.
Thought the files might have been empty, opened on Ubuntu and head -n2 function worked fine for each file, so I don't think it's an issue with the files.
My data was originally stored on an online shared network drive, moved files to local computer to eliminate any possibility for path errors. Still have the error message.
Have tried the same function with a number of different files, and I always have the same error message. So I think the issue is with how R studio is reading the files, and not the files themselves.
Would really appreciate some support with this, at the end of my PhD trying to analyse the last piece of my data and really struggling with this. Thanks in advance for any feedback!
> library(IsoPops)
Welcome to IsoPops version 0.3.1.
> transcript_AD3 <- "C:/R_Package_for_IsoSeq/IsoPops/IsoPops_Data/AD3-hq_transcripts.fasta"
> abundance_AD3 <- "C:/R_Package_for_IsoSeq/IsoPops/IsoPops_Data/AD3_Collapsed_Filtered_Isoform_Counts.abundance.txt"
> GFF_AD3 <- "C:/R_Package_for_IsoSeq/IsoPops/IsoPops_Data/AD3-collapse_isoforms.gff"
> rawDB <- compile_raw_db(transcript_AD3, abundance_AD3, GFF_AD3)
[1] "Loading sequences..."
Error in system(command = paste("head -n1 ", filename, step = ""), intern = T) :
'head' not found
I am trying to convert a Tensorflow Object Detection model(ssd-mobilenet-v2-fpnlite, from TensorFlow 2 Detection Model Zoo) to TFLite. First of all, I train the model using the model_main_tf2.py and then I use the export_tflite_graph_tf2.py to export a saved model(.pb). However, when it comes to convert the .pb file to .tflite it throws this error:
OSError: SavedModel file does not exist at: /content/gdrive/My Drive/models/research/object_detection/fine_tuned_model/saved_model/saved_model.pb/{saved_model.pbtxt|saved_model.pb}
To convert the .pb file I used:
import tensorflow as tf
SAVED_MODEL_PATH = os.path.join(os.getcwd(),'object_detection', 'fine_tuned_model', 'saved_model', 'saved_model.pb')
# SAVED_MODEL_PATH: '/content/gdrive/My Drive/models/research/object_detection/exported_model/saved_model/saved_model.pb'
converter = tf.lite.TFLiteConverter.from_saved_model(SAVED_MODEL_PATH)
converter.optimizations = [tf.lite.Optimize.DEFAULT]
converter.experimental_new_converter = True
converter.target_spec.supported_ops = [tf.lite.OpsSet.TFLITE_BUILTINS, tf.lite.OpsSet.SELECT_TF_OPS]
tflite_model = converter.convert()
open("detect.tflite", "wb").write(tflite_model)
or "tflite_convert" from command line, but with the same error. I also tried to run it with the latest tf-nightly version as it suggests here, but the outcome is the same. I tried to pass the path with various ways, it seems like the .pd is not well written (not the right file). Is there a way to manage to convert the model to tflite so as to implement it to android? Thank you!
Your saved_model path should be "/content/gdrive/My Drive/models/research/object_detection/fine_tuned_model/saved_model/". It is the folder instead of files in that folder
For quick test, try to type in terminal
tflite_convert \
--saved_model_dir="path to saved_folder" \
--output_file="path to tflite file u want to save"
I don't have enough reputation to just comment but the problem here seems to be your SAVED_MODEL_PATH.
You could try to hardcode the path and remove the .pb file. I don't remember exactly what's the trick here but it's definitively due to the path
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.
The ZevRoss blog is as follow:
http://zevross.com/blog/2014/04/11/using-r-to-quickly-create-an-interactive-online-map-using-the-leafletr-package/
The code with error is:
# ----- Write data to GeoJSON
leafdat<-paste(downloaddir, "/", filename, ".geojson", sep="")
writeOGR(subdat, leafdat, layer="", driver="GeoJSON")
And the error is:
Error in writeOGR(subdat, leafdat, layer = "", driver = "GeoJSON") :
GDAL Error 3: Cannot open file 'd:/Leaflet/County_2010Census_DP1.geojson'
Because I am a freshman in R, I searched for this problem a lot and didn't get any good answer.
I am using Rstudio R version 3.1.1(2014-07-10) on windows 7 32bit.
My rgdal version is 0.9-1.
The other code in the blog runs successfully, this sentence seems to be the only difficult point.
You could create GeoJSON using leafletR package:
library('leafletR')
Your_GeoJSON <- toGeoJSON(data=YourData, dest=getwd())
I've tried to find a solution for this mysterious error for some time.
Eventually I found this post on the Gdal package errors' tickets site that clarified the problem and gave a solution.
Basically the problem is in the interface between rgdal and Gdal (Gdal changed their way to work and the latest version of rgdal hasn't watched up yet):
writeOGR() calls ogrCheckExists("foo.geojson") to check first if the file exists before creating a new dataset.
In the 1.11 version the OGR GeoJSON driver will emit an error message that this file doesn't exists, whereas previous version didn't emit an error message.
rgdal catches this error as a fatal one and doesn't go to the writing step. This should be fixed in rgdal.
Meanwhile you have an easy workaround : add check_exists = FALSE as a parameter to writeOGR()
Therefore the following code will work:
writeOGR(spDf,'foo.geojson','spDf', driver='GeoJSON',check_exists = FALSE)
Of course if there is already a geojson file with the chosen name at the location writeOGR still fails.
Even though you already have a 'd:' drive on your computer and you have permission to write to that drive, try the following:
--------------------------------
leafdat<-paste(downloaddir, "/", ".geojson", sep="")
> leafdat
> "d:/Leaflet/.geojson"
writeOGR(subdat, leafdat, layer="", driver="GeoJSON")
--------------------------------
Then you may get ".geojson" file on "d:/Leaflet". Change the file name ".geojson" to "County_2010Census_DP1.geojson".
I tried to use get_rollit_source from the RcppRoll package as follows:
library(RcppRoll)
get_rollit_source(roll_max,edit=TRUE,RStudio=TRUE)
I get an error:
Error in get("outFile", envir = environment(fun)) :
object 'outFile' not found
I tried
outFile="C:/myDir/Test.cpp"
get_rollit_source(roll_max,edit=TRUE,RStudio=FALSE,outFile=outFile)
I get an error:
Error in get_rollit_source(roll_max, edit = TRUE, RStudio = FALSE, outFile = outFile) :
File does not exist!
How can fix this issue?
I noticed that the RcppRoll folder in the R library doesn't contain any src directory. Should I download it?
get_rollit_source only works for 'custom' functions. For things baked into the package, you could just download + read the source code (you can download the source tarball here, or go to the GitHub repo).
Anyway, something like the following should work:
rolling_sqsum <- rollit(final_trans = "x * x")
get_rollit_source(rolling_sqsum)
(I wrote this package quite a while back when I was still learning R / Rcpp so there are definitely some rough edges...)