OMNETPP simulation of WVSN
I am facing error,
Error: Error loading NED sources from .': NED error in fileThroughputTest.ned': declared package node.application.throughputTest' does not match expected packageCastalia-files.input.src.node.application.throughputTest'.
Related
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.
I am tryin to use the "smapr" package on R to download and process the SMAP data following the set of examples from this website, but at the first step only getting this error
Error in rvest::html_table(nodes)[1] : subscript out of bounds.
Despite installing all the necessary packages and details.
I am trying to run the following lines of code:
tree <- read.nexus("~/Dropbox/Billfishes/Analysis/Phylogenies/Fish_12Tax_time_calibrated.tre");
characterTable <- read.csv("~/Dropbox/Billfishes/Analysis/CodingTableThresh95.csv", row.names = 1);
treeWData <- treedata(tree, characterTable, sort = T);
When I ran this code last week, it worked. I then updated all my packages as part of routine maintenance, and now I get this error:
Error in integer(max(oldnodes)) : vector size cannot be infinite
In addition: Warning message:
In max(oldnodes) : no non-missing arguments to max; returning -Inf
I've tried rolling back to previous versions of R (I'm currently running R version 3.4.0 in RStudio 1.0.143; geiger is version 2.0.6), reading the tree in as a Newick, and trying other tree files, always resulting in the same error. When I try using other tree and character datasets, I do not get the error.
Any ideas what this error means, and/or how to get this code to run without throwing this error?
After careful error checking, I discovered that the taxon names in the phylogeny file were separated by underscores, whereas the taxon names in the table used camel caps. Thus, the error was thrown because no taxa in the phylogeny mapped to the character table.
Working through a download script for CPS data found here. Using the script verbatim, per recent update, except for the Java modification that I added for my environment (below) to fix a previous error in loadnamespace. While I am familiar with the basics of R, this is my first foray into MonetDBLite.
# configure Java
if (Sys.getenv("JAVA_HOME")!="")
Sys.setenv(JAVA_HOME="")
library(rJava)
Now I am getting the following error, which generally comes after 380,000 of the 400,000 cps asec lines are processed.
Warning message:
In readLines(url) :
incomplete final line found on 'http://thedataweb.rm.census.gov/pub/cps/march/asec2015early_pubuse.dd.txt'
Error in dbConnect(MonetDBLite::MonetDBLite(), dbfolder) :
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': Error: 'MonetDBLite' is not an exported object from 'namespace:MonetDBLite'
MonetDBLite has just been updated on CRAN, please reinstall.
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’