Keep getting the following warning:
"Warning message:
In data(VEMCOdata) : data set ‘VEMCOdata’ not found"
I'm new to R. I set up all my files exactly how the package VTrack specified. I set my working directory, load my first data set then ue the command >data(xx) and keep getting the same warning message.
setwd("C:/Users/gwhite/Desktop")
library(VTrack)
VEMCOdata <- read.csv('VEMCOdata_2014.csv')
data(VEMCOdata)
Warning message:
In data(VEMCOdata) : data set ‘VEMCOdata’ not found
Related
My code is
multiome <- load_object(file.path(dataset, "C:/Users/s/Desktop/Shahid/MOJITOO DATASETS/PBMC_Multiome.Rds"))
I get the following error:
Error in open.connection(3L, "rb") : cannot open the connection
In addition: Warning message:
In open.connection(3L, "rb") :
cannot open file 'kidney/C:/Users/s/Desktop/Shahid/MOJITOO DATASETS/PBMC_Multiome.Rds': Invalid argument
Called from: open.connection(3L, "rb")
I want to implement the MOJITOO single cell integration model. I get the error shown above.
I have bigquery some table. bq_table_download functions work for most of the table, however, it shows failed to parse errors with 1 table.
bigrquery::bq_auth()
sql_query=paste0("select * from `project_id.dataset.table_name`")
bq_table_ext=bq_table_download(bq_project_query(project_id, sql_query))
In order to solve this I have also used as suggested bq_table_download have download quota limit.
options(scipen = 20)
However, still, I am unable to figure what is an issue.
Here is snapshot of error code
Error in bq_parse_files(schema_path, c(path_first_chunk, chunk_plan$dat$path), :
Failed to parse '/tmp/Rtmpjd5eQN/bq-download-8650ad590.json'
Calls: ... master_table_base -> bq_table_download -> bq_parse_files
In addition: Warning messages:
1: In writeBin(result$content, con) : problem writing to connection
2: In writeBin(result$content, con) : problem writing to connection
Execution halted
Using the attached dataset in RStudio, I'm getting the following error message:
Error in readLines(file, encoding = encoding) :
(converted from warning) line 1 appears to contain an embedded nul
After the following code:
txn = read.transactions(file="ItemList22.xlsx", rm.duplicates=TRUE, format="basket",sep=",",cols=1,quote = "\"'", skip = 0,encoding="unknown");
I'm trying to set the data up for Apriori analysis using the 'arules' package. Per other StackOverflow posts and CRAN documentation, I've tried adding encoding options to the above code... but they don't seem to work.
What am I doing wrong?
Currently I am trying to understand DEXSeq package. I have a design tsv file and 7 files which contains Counts. Now would like to run the following command
library("DEXSeq");
design=read.table("dexseq_design.tsv", header=TRUE, row.names=1);
ecs = DEXSeqDataSetFromHTSeq(countfiles=c("M0.txt", "M1.txt", "M2.txt", "M3.txt", "M4.txt", "M5.txt", "M6.txt", "M7.txt"), design=design, flattenedfile="genome.chr.gff");
The last command gives and error
Error in class(sampleData) %in% c("data.frame") :
error in evaluating the argument 'x' in selecting a method for function '%in%':
Error: argument "sampleData" is missing, with no default
What does this error means and how to fix it? While loading the package DEXSeq there was a warning
Warning message:
replacing previous import by ‘ggplot2::Position’ when loading ‘DESeq2’
I can't save.ffdf or move.ffdf. Also, the deprecated ffdfsave is broken.
require(ff);require(ffbase)
x <- data.frame(matrix(rnorm(5*5),ncol=5))
x <- as.ffdf(x)
save.ffdf(x,getwd())
I will get the following error:
Error infilename<-.ff(tmp, value = "/home/... Deleted .../path$X0.0.ff") :
ff file rename from '/tmp/RtmpasUciV/ffdf346c5f0daaea.ff' to '/home/... Deleted .../path$X0.0.ff' failed
The only thing that will work is:
require(ff);require(ffbase)
x <- data.frame(matrix(rnorm(5*5),ncol=5))
x <- as.ffdf(x)
save.ffdf(x,tempfile())
Note that when I call this on my local terminal it works. It's just when I try this on a remote server it does not work.
I will also get the error underneath the above error:
In addition: Warning message:
In file.rename(oldnam, value) :
cannot rename file '/tmp/RtmpasUciV/ffdf346c5f0daaea.ff' to '/home/... Deleted .../path$X0.0.ff', reason 'Invalid cross-device link'