I'm trying to create a plot using boxcox function from package MASS.
but it's creating an rapache error.
The r code:
<%
csvDF<- read.csv(GET$name1, header=TRUE)
a<-lm(csvDF[,GET$col_variable]~1)
require(MASS)
filename1 <- paste(tempfile(tmpdir='/var/www/images'), '.png', sep='')
png(filename1)
bx<-boxcox(a)
dev.off()
%>
**GET$name1 is the csv data file address.
**GET$col_variable is the variables column.
When I lose the "bx<-boxcox(a)" line the error disappear, so I guess that the boxcox causes the error.
Here are the rapache errors:
RApache Warning/Error!!!
Error in eval(expr, envir, enclos) : object 'csvDF' not found
RApache Warning/Error!!!
In addition:
RApache Warning/Error!!!
Warning messages:
RApache Warning/Error!!!
1: In readLines(icon, 1) : incomplete final line found on '/var/www/brew/sampleplan/step5_box_cox.php'
RApache Warning/Error!!!
2: In readLines(icon, 1) : incomplete final line found on '/var/www/brew/sampleplan/step5_box_cox.php'
RApache Warning/Error!!!
3: In readLines(icon, 1) : incomplete final line found on '/var/www/brew/sampleplan/step5_box_cox.php'
RApache Warning/Error!!!
4: In readLines(icon, 1) : incomplete final line found on '/var/www/brew/sampleplan/step5_box_cox.php'
RApache Warning/Error!!!
5: In readLines(icon, 1) : incomplete final line found on '/var/www/brew/sampleplan/step5_box_cox.php'
RApache Warning/Error!!!
Function brew returned an object of 'try-error'. Returning HTTP response code 500.
I will be gratefull for any suggestion.
It is very difficult to give a complete answer because your whole setup isn't available. The error message (as opposed to the warnings; worry about them later) is the variable csvDF isn't found. It is unclear whether this error happens before or after you call read.csv. Either way, the problem isn't the call to boxcox.
Also note that lm has a data argument that could make your code clearer. Try something like
lm_formula <- as.formula(paste(col_variable, "1", sep = "~"))
a <- lm(lm_formula, data = csvDF)
You would also benefit from separating out code that reads data, calculates statistics, creates plots and writes plots to file.
Related
Using the syuzhet package in R, the following works but returns a warning message:
object <- get_text_as_string("path/name.txt")
When I put this in a function, it returns the same warning error but does NOT change the value of object:
gen <- function(file){
object <- get_text_as_string(file)
}
gen("path/name.txt")
This is the warning message, if it matters:
Warning message:
In readLines(path_to_file) :
incomplete final line found on 'path/name.txt'
...but again, I get that from get_text_as_string() when used outside of the function, but it DOES change the value of object.
Anyone have any advice? There must be something I don't understand about functions?
(I've looked for similar questions/answers, if I've missed the right one I'd be happy to just be directed there.)
I have been getting this error for the first time for commands that used to run well before:
# conversion from char to numeric:
as.numeric(df$col) -> df$col
Error: (converted from warning) NAs introduced by coercion
# running metafor
rma(yi, vi, data=r1s2)
Error: (converted from warning) Studies with NAs omitted from model fitting.
The issue must be with the R environment as these commands are running perfectly on a different computer. The only wrong I can think of is installing a package from GitHub or updating R a few hours ago. The only relevant answer I've found so far is also not working:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
This seems to be a warning level issue. If the warning level is 2, warnings become errors. From the documentation, my emphasis.
warn:
integer value to set the handling of warning messages. If warn is negative all warnings are ignored. If warn is zero (the default) warnings are stored until the top–level function returns. If 10 or fewer warnings were signalled they will be printed otherwise a message saying how many were signalled. An object called last.warning is created and can be printed through the function warnings. If warn is one, warnings are printed as they occur. If warn is two (or larger, coercible to integer), all warnings are turned into errors.
old_ops <- options(warn = 2)
warning("this is a warning")
#> Error in eval(expr, envir, enclos): (converted from warning) this is a warning
x <- "a"
as.numeric(x)
#> Error in eval(expr, envir, enclos): (converted from warning) NAs introduced by coercion
options(old_ops)
Created on 2022-06-25 by the reprex package (v2.0.1)
If you say that
The issue must be with the R environment as these commands are running perfectly on a different computer.
then check if you have a file named .RData in your R startup directory. If you have one, then you probably set the warning level in a previous session and now it is being restored every time you run R. Delete this file and this behavior will go away.
See also this SO post.
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'd like to create warning/error log for the R script.
Please see below example:
setwd(tempdir())
zz <- file("all.Rout", open="wt")
sink(zz, type="message")
for (i in 1:30){
log(i-50)
}
sink(type="message")
close(zz)
I was expecting that it will enlist all warnings:
Warning messages:
1: In log(i - 50) : NaNs produced
2: In log(i - 50) : NaNs produced
3: In log(i - 50) : NaNs produced
However for the loop i in 1:30 there is only one line in the all.rout file:
There were 30 warnings (use warnings() to see them)
Any idea how to fix it?
I have created the code based on another topic:
Output error/warning log (txt file) when running R script under command line
Try options(warn=1)
From ?options:
'warn': sets the handling of warning messages. If 'warn' is
negative all warnings are ignored. If 'warn' is zero (the
default) warnings are stored until the top-level function
returns. If 10 or fewer warnings were signalled they will be
printed otherwise a message saying how many were signalled.
An object called 'last.warning' is created and can be printed
through the function 'warnings'. If 'warn' is one, warnings
are printed as they occur. If 'warn' is two or larger all
warnings are turned into errors.
Trying to use the latest version of methylSig package (0.3.2), and getting an error when using the methylSigCalc function.
I get a cryptic error message after it figures out the number of loci:
Total number of bases: 2.59m
Error in result[, 3] : subscript out of bounds”
I tried running the code of the methylSigCalc function line by line, and the first error I encounter is when it gets to the methylSig_dataProcess function (below is the error after specifying just one core to try to get a useful error message):
Error in do.call(rbind, lapply(which(validLoci),
methylSig_dataProcess, : error in evaluating the argument 'args' in
selecting a method for function 'do.call': Error in match.fun(FUN) :
object 'methylSig_dataProcess' not found
It does seem that methylSig_dataProcess is now missing from the package.
Any suggestions on where I might be going wrong?
Many thanks,
gogatea