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.
Related
I am trying to run dada2 within RStudio. Normally I would run it in Windows. However because I want to run cutadapt as well I have had to create a Linux VM. With some help I now have dada2 and cutadapt installed on my VM. I have copied over my R code which works in RStudio in Windows. I have editted the code on my VM so that it points towards the correct directories, e.g. replaced "c:\Rtemp" with "~/Rtemp". I believe I have done this correctly as RStudio reads in dada2 and then my files just like it does when I start the script in RStudio in Windows. However I then get error messages that I don't get when I run the script in RStudio in windows.
fnFs <- sort(list.files(path, pattern="_R1_001.fastq", full.names = TRUE))
fnRs <- sort(list.files(path, pattern="_R2_001.fastq", full.names = TRUE))
sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)
plotQualityProfile(fnFs[1:2])
Error in (function (cond) :
error in evaluating the argument 'dirPath' in selecting a method for function 'qa': IncompatibleTypes
message: error in evaluating the argument 'x' in selecting a method for function 'which': error in evaluating the argument 'x' in selecting a method for function 'alphabetFrequency': invalid class “BStringSet” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
There are no "install" errors so I don't think the problem is missing installs. Is this error message indicating a problem with the amount of memory on my VM?
I recently ran into this problem while working through the dada2 tutorial.
I fixed it by loading up library(Biostrings) before loading dada2. I was under the impression that dada2 automatically loaded up Biostrings, but this was the fix. Hopefully it works for you.
I'm quite new to R and I got an assignment that includes a sourcecode.
Part of the source code includes the following line:
library(preprocessCore)
Then I have in my source code a definition of the following function:
quantile.normalize.raw.gtex <- function(edata.mat)
{
norm_edata = normalize.quantiles(as.matrix(edata.mat))
rownames(norm_edata) = rownames(edata.mat)
colnames(norm_edata) = colnames(edata.mat)
return(norm_edata)
}
Finally, I have an object being initialized to the output of this function, after sending a predefined parameter:
tissue.edata.qn = quantile.normalize.raw.gtex(tissue.edata)
From what I understand, the library function is supposed to include the function normalize.quantiles, which is called in the function that is defined in my source code.
However, when I run the line library(preprocessCore) I get the following error:
Error in library(preprocessCore) :
there is no package called ‘preprocessCore’
I also tried to run the rest of the code and got the error:
Error in normalize.quantiles(as.matrix(edata.mat)) :
could not find function "normalize.quantiles"
I looked for the preprocessCore online and eventually I tried to write install.packages("preprocessCore"), but I got a warning message that this package is only available in version 3.6.0 of R, even though I checked and this is the version that I have.
If somebody has any idea what the problem is, I will appreciate your help.
Thanks in advance
The preprocessCore package is available in Bioconductor. So, to install it, you need the following lines:
source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")
After that, you can load the package using library(preprocessCore)
Hope it helps.
I tried to run the code in Chapter 7 Data mining with R learning with case study book but I got an error in following line:
rankWorkflows(svm, maxs = TRUE)
The error was:
Error in as.character.default(X[[i]], ...) : no method for coercing
this S4 class to a vector
Then I searched on the internet and found following solution:
importMethodsFrom(GenomicRanges, as.data.frame)
and again again I got a new error:
Error: could not find function "importMethodFrom"
I searched a lot but I got nothing :(
You can try using library(sos) to find the packages where your function is located.
library(sos)
findFn("replaceherewithyourfunction")
Based on the answer of #Bea, there does not seem to be a importMethodsFrom anywhere in R. My guess is you found the call in a NAMESPACE file. Those files have different syntax than normal R scripts.
If you want to load a specific function from an R package (rather than all functions from a package), you can use libraryname::functionname instad of functionname in your code. In your case, replace as.data.frame with GenomicRanges::as.data.frame
If this does not work (for example because you don't have as.data.frame anywhere in your code), you can also load the whole GenomicRanges library with library(GenomicRanges)
The following example code in the documentation of the Thinknum package
install.packages("Thinknum")
library(Thinknum)
thinknumdata = Thinknum("total_revenue(goog)")
leads on my machine to the following error:
Error in Thinknum("total_revenue(goog)") : Requested Expression does not exist.
It would help me a lot, if one or more people could run the example code on another machine.
I have written the Boggler package which includes a Play.Boggle() function that calls, on line 87, a progress bar script using shell:
shell(cmd = sprintf('Rscript.exe R/progress_bar.R "%i"', time.limit + 1), wait=FALSE)
Everything works fine when sourcing the files individually and then calling the main Play.Boggle() function, but when I try to check/build the package (under Win7-64 using RStudio), I get a failure message -- here's what the 00install.out reports:
** preparing package for lazy loading
Warning in eval(expr, envir, enclos) : NAs introduced by coercion
Error in time.limit:0 : NA/NaN argument
To make sure the argument "%i" (time.limit + 1) was correctly passed to the progress_bar.R, I added a cat(time.limit) to the script (commenting the rest out to make sure the package would build without any errors) and directed its output to a log file like this:
'Rscript.exe R/progress_bar.R "%i" > out.log'
Conclusion: the time limit is indeed passed along as expected. So I can't figure out why I get this "NA/NaN argument" error message. It must have something to do with lazy loading, concept that I haven't fully got my head around yet.
So my question is: what can I do to successfully check/build this package with full functionality (including progress_bar.R)?
Note: On github, the progress_bar.R script is there but all its content is commented out so that the package can successfully be installed. The shell(...) function call is still active, doing nothing but executing an empty script.
So the problem arises when trying to build or check, in which case all R scripts are executed, as pointed out by Roland. A simple workaround allows the package to check/build without any problems. The fix is just to add to the progress_bar.R the following lines after it tries to recuperate the commandargs (lines 10-11):
if(time.limit %in% c(NA, NaN))
time.limit <- 10 # or any minimal number
There's surely other ways to go about this. But this being a game programmed for fun, I'll happily go with that patch. Hopefully this can be of help to someone down the road and I won't have wasted 50 precious rep points in vain for that bounty! :D