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.
Related
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.
I am using package installr version 0.17.0 to update R and related packages. However, I get the following error message when I typed updater():
Error in strsplit(version_with_dots, "\\.")[[1]] :
subscript out of bounds
How can I deal with this situation?
The current version of R is "3.2.4 Revised". installr appears to be having trouble with the " Revised" part of the name. The bug has been fixed in the latest version of the package.
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'm trying to use root from the ape package in R, but I keep getting the following error:
Error in FUN(X[[i]], ...) : object 'fuseRoot' not found
Here is the code that isn't working:
mammal.trees <- lapply(mammal.trees, root, "Gal", resolve.root=TRUE)
I'm stumped because the same code works for another multiPhylo object just fine.
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