I'm using dada 2 version ‘1.22.0’ on windows 10, i have list of compressed (.gz ) fastq files, when i use the function filterAndTrim i get this error message :
Error in add(bin) : record does not start with '#'
But when i want to see if i can read th .gz file with library(ShortRead) :
library(ShortRead)
fn <- "path/to/example.fastq.gz"
reads <- readFastq(fn)
it doesn't give any error message message
I don't understand why the function filterAndTrim give the error message
Error in add(bin) : record does not start with '#'
Do you have any solution?
I am trying to use pdf2image, but I am getting this error:
PDFPageCountError: Unable to get page count.
I/O Error: Couldn't open file 'C:\Users\user_name\Desktop\folder_name\folder2_name\folder3_name\007-084841-1 to 31 Dec'22': No error.
It is confusing as it doesn't give any error, it just says 'No error'
My code is:
doc = convert_from_path("C:\\Users\\user_name\\Desktop\\folder_name\\folder2_name\\folder3_name\\007-084841-1 to 31 Dec'22")
path, fileName = os.path.split("C:\\Users\\user_name\\Desktop\\folder_name\\folder2_name\\folder3_name\\007-084841-1 to 31 Dec'22")
fileBaseName, fileExtension = os.path.splitext(fileName)
for page_number, page_data in enumerate(doc):
txt = pytesseract.image_to_string(Image.fromarray(page_data)).encode("utf-8")
print("Page # {} - {}".format(str(page_number),txt))
Can anyone help me please?
I don't know what to try as the error message just says Unable to open...: No error
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! Error in .shlib_internal(commandArgs(TRUE)) :
C++14 standard requested but CXX14 is not defined
Calls: <Anonymous> -> .shlib_internal
Execution halted
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command 'C:/PROGRA~1/R/R-36~1.0/bin/x64/R CMD SHLIB file1a1860a0379.cpp 2> file1a1860a0379.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection
Some non-English page said that we can overcome by executing the following R script, but it did not work in my case:
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR))
dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M))
file.create(M)
cat("\nCXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function",
"CXX14 = g++ -std=c++1y",
file = M, sep = "\n", append = TRUE)
The above R script is same as in the following page:
https://github.com/stan-dev/rstan/issues/569
I tried to uninstall and install according to the following page, but the above error occurred.
Rstan installation: https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
REF; https://github.com/stan-dev/stan/issues/1613
ref: https://github.com/stan-dev/rstan/issues/633
For me, the issue has been solved by adding manually the following line into the file .R/Makevars.win.
CXX14 = "C:\Rtools\mingw_64\bin\g++.exe"
i'm trying to run a API request for a number of parameters with the lapply function in R.
However, when i run this function, i get the error " Error in file(con, "r") : cannot open the connection"
Google suggests using setInternet2(TRUE) to fix this issue, however, i get the error: Error: 'setInternet2' is defunct.
See help("Defunct"
localisedDestinationNameForGivenLang <- function (LocationId) {
gaiaURL <- paste0("https://URL/",LocationId, "?geoVersion=rwg&lcid=", "1036",
"&cid=geo&apk=explorer")
print(LocationId)
localisation <- fromJSON(gaiaURL)
}
lapply(uniqueLocationId, localisedDestinationNameForGivenLang)
Can someone suggest a fix please?
Here's a sample of how you could identify which sites are throwing errors while still getting response from the ones that don't:
urls = c("http://citibikenyc.com/stations/test", "http://citibikenyc.com/stations/json")
grab_data <- function(url) {
out <- tryCatch(
{fromJSON(url)},
error=function(x) {
message(paste(url, x))
error_msg = paste(url, "threw an error")
return(error_msg)
})
return(out)
}
result <- lapply(urls, grab_data)
result will be a list that contains API response for urls that work, and error msg for those that don't.
I heard about exception handling first time in python two days ago and consequently I want to apply here in R. I had a look at a number of questions post either here in stack overflow or some other online Q&As but I am still really confused in using it.
I would really appreciate if someone can answer it with this simple example so later on I can apply it to my questions.
For example I have 3 data files with file names shown below; and the first file is a 0 bytes empty file. What I can do to continue run the loop for all files and the number extracted from the empty file can be expressed as NA?
> output_names_hdf5_list[1:5]
[1] "simulation-results fL=0.1,fks=1,fno=0.1,fnc=0.1,fr=0.1,fs=0.1.hdf5"
[2] "simulation-results fL=0.1,fks=1,fno=0.1,fnc=0.1,fr=0.1,fs=1.05.hdf5"
[3] "simulation-results fL=0.1,fks=1,fno=0.1,fnc=0.1,fr=0.1,fs=2.hdf5"
for (i in 1:5){
channelflow_outlet[,i]=h5read(paste(outputdir, output_names_hdf5_list[i], sep=""),"Channel")$Qc_out[460,][2:100]
}
With try function I can manage to run the program without stuck in an error message but when I replace the argunment with channelflow_outlet[,i]= h5read(....) inside try function, it just returns error.
for (i in 1:5){
try(h5read(paste(outputdir, output_names_hdf5_list[i], sep=""),"Channel")$Qc_out[460,][2:100])
}
Without error handling, it will have a error message like this.
> h5read(paste(outputdir, output_names_hdf5_list[1], sep=""),"Channel")$Qc_out[460,][2:100]
HDF5: unable to open file
Error in h5checktypeOrOpenLoc(file, readonly = TRUE) :
Error in h5checktypeOrOpenLoc(). File 'D:/Data/Mleonard/pytopkapi.staged.makefile/RunModel/Output/3x6-729-04072014/simulation-results fL=0.1,fks=1,fno=0.1,fnc=0.1,fr=0.1,fs=0.1.hdf5' is not a valid HDF5 file.
>
I hope my code helps. For those messages in the code, you can delete them if you want. They are here purely to help you see where it shows warning or error.
setwd("D:/Dropbox/Test/"); outputdir = "D:/Dropbox/Test/"
output_names_hdf5_list=c("simulation-results fL=0.1,fks=1,fno=1.05,fnc=1.05,fr=1.05,fs=1.05.hdf5",
"simulation-results fL=0.1,fks=1,fno=1.05,fnc=2,fr=1.05,fs=1.05.hdf5",
"simulation-results fL=0.1,fks=1,fno=2,fnc=1.05,fr=0.1,fs=1.05.hdf5",
"simulation-results fL=0.1,fks=1,fno=2,fnc=1.05,fr=2,fs=2.hdf5",
"simulation-results fL=0.5,fks=1,fno=2,fnc=2,fr=0.1,fs=1.05.hdf5")
channelflow_outlet = matrix(NA, nrow=100, ncol=5)
hdf5_list_reading_tool= function(output_names_hdf5_list) {
out = tryCatch(
{
message("This is the 'try' part")
h5read(paste(outputdir, output_names_hdf5_list, sep=""),"Channel")$Qc_out[460,][2:100]
},
error=function(cond) {
message("Here's the original error message:")
message(cond)
return(rep(NA,100))
},
warning=function(cond) {
message("Here's the original warning message:")
message(cond)
return(rep(NA,100))
},
finally={
message(paste("Processed URL:", output_names_hdf5_list))
message("Some other message at the end")
}
)
return(out)
}
channelflow_outlet=sapply(output_names_hdf5_list, hdf5_list_reading_tool)