I am trying to load "sample.RData" file in R. The error it gives is
Error in load("sample.RData") : bad restore file magic number (file
may be corrupted) -- no data loaded In addition: Warning message: file
‘sample.RData’ has magic number 'RDX3' Use of save versions prior to
2 is deprecated
I checked many solutions like, to use save() instead of load etc. but not successful. Please recommend any solution.
Are you trying to load like this:
load("your_directory/object_name.RData")
Related
I'm trying to use the package bambu to quantify gene counts from bam files. I am using my university's HPC, so I have written an R script and a batch submission file to launch it.
When the script gets to the point of running the bambu function, it gives the following error:
Start generating read class files
| | 0%[W::hts_idx_load2] The index file is older than the data file: ./results/minimap2/KD_R1.sorted.bam.bai
[W::hts_idx_load2] The index file is older than the data file: ./results/minimap2/KD_R3.sorted.bam.bai
[W::hts_idx_load2] The index file is older than the data file: ./results/minimap2/WT_R1.sorted.bam.bai
[W::hts_idx_load2] The index file is older than the data file: ./results/minimap2/WT_R2.sorted.bam.bai
|================== | 25%
Error: BiocParallel errors
element index: 1, 2, 3
first error: cannot open the connection
In addition: Warning message:
stop worker failed:
attempt to select less than one element in OneIndex
Execution halted
So it looks like BiocParallel isn't happy and cannot open a certain connection, but I'm not sure how to fix this?
This is my R script:
#Bambu R script
#load libraries
library(Rsamtools)
library(bambu)
#Creating files
bamFiles<- Rsamtools::BamFileList(c("./results/minimap2/KD_R1.sorted.bam","./results/minimap2/KD_R2.sorted.bam","./results/minimap2/KD_R3.sorted.bam","./results/minimap2/WT_R1.sorted.bam","./results/minimap2/WT_R2.sorted.bam","./results/minimap2/WT_R3.sorted.bam"))
annotation<-prepareAnnotations("./ref_data/Homo_sapiens.GRCh38.104.chr.gtf")
fa.file<-"./ref_data/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
#Running bambu
se<- bambu(reads=bamFiles, annotations=annotation, genome=fa.file,ncore=4)
se
seGene<- transcriptToGeneExpression(se)
#Saving files
save.file<-tempfile(fileext=".gtf")
writeToGTF(rowRanges(se),file=save.file)
save.dir <- tempdir()
writeBambuOutput(se,path=save.fir,prefix="Nanopore_")
writeBambuOutput(seGene,path=save.fir,prefix="Nanopore_")
If you have any ideas on why this happens it would be so helpful! Thank you
I think that #Chris has a good point. Under the hood it seems likely that bambu is running htslib based on those warnings. While they may indeed only be warnings, I would like to know what the results would look like if you ran this interactively.
This question is hard to answer right now as it's missing some information (what do the files look like, a minimal reproducible example, etc.). But in the meantime here are some possibly useful questions for figuring it out:
what does bamFiles look like? Does it have the right number of read records? Do all of those files have nonzero read records? Are any suspiciously small?
What are the timestamps on the bai vs bam files (e.g. ls -lh /results/minimap2/)? Are they about what you'd expect or is it wonky? Are any of them (say, ./results/minimap2/WT_R2.sorted.bam.bai) weirdly small?
What happens when you run it interactively? Where does it fail? You say it's at the bambu() call, but how do you know that?
What happens when you run bambu() with ncores=1?
It seems very likely that this is due to a problem with the files, and it is only at the biocParallel step that the error is bubbling up to the top. Many utilities have an annoying habit of being happy to accept an empty file, only to fail confusingly without informative error messages when asked to do something with the empty file.
You might also consider raising an issue with the developers.
(why the warning is only possibly a problem: The index file sometimes has a timestamp like that for very small alignment files which are generated and indexed programmatically, where the indexing step is near-instantaneous.)
So I'm rather new to R, and I'm learning how to mine text from this handy website: https://eight2late.wordpress.com/2015/05/27/a-gentle-introduction-to-text-mining-using-r/
I do have my own text set of .doc, .docx, and .xlsx files and I'm trying to mine them. They're located in a folder in my working directory called 'files', but I have already encountered an error after simply writing a few lines of code.
The code I have so far is:
library(tm)
library(readtext)
data = readtext('files')
At this point, after waiting for 25 seconds or so, I get the error:
Error: System call to 'antiword' failed (1): The Big Block Depot is damaged
and the code stops running there.
I have tried searching online for solutions but it seems like a fairly rare error and so I only found 1 possible solution at https://github.com/ropensci/antiword/issues/1 but that did not work for me.
This solution suggested that one of my files were corrupt, and suggested using the code
fixInNamespace(antiword, pos="package:antiword")
to change the error to a warning to not interrupt the reading of the files. I tried that, and at first it raised the error of
Error in as.environment(pos):
no item called "package:antiword" on the search list
After which, I loaded the antiword library with a library(antiword) and changed the stop( to a warning(. However, when I ran the data = readtext('files') line again, it immediately raised the error
Error in is_windows() : could not find function "is_windows"
I'm at a loss here! Any help would be appreciated. Should I be using another package in this case?
I had the same problem with my code, where I tried to get a doc. file in R. I also used the readtext library. What helped me was converting the Word documents I was trying to get into R from doc. to docx. When I ran the same code after it worked.
I am a Bioinformatics student and pretty much an amateur R user. I have gone through almost the whole of the internet without getting any examples for the working of this package except the documentation provided by 'Bioconductor'-website. I am currently working on the 'AllelicImbalance' package provided by 'Bioconductor' for handling genomics data such as large 'BAM' files to find specific allelic positions and then analyzing them. I have gone ahead with their tutorial by creating a BAM format file. Then later to operate the file, I have set my working directory where my files have been saved.
The code for operating is -
> library(AllelicImbalance)
> searchArea<-GRanges(seqnames = c("17"), ranges = IRanges(79478301, 79478361))
> pathToFiles<-system.file("ERR009135.bam", package = "AllelicImbalance")
> reads<-impBamGAL(pathToFiles, searchArea, verbose=FALSE)
I get an error after the last command which says -
Error in .local(UserDir, ...) : No bam files found in
In addition: Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
path[1]="": The filename, directory name, or volume label syntax is incorrect
The samples that I have used are present in here and are paired-end 'fastqc' files - ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR009/ERR009135
To download these files, a stable and fast internet connection is required. Later I converted these files to the 'BAM' format using the 'Linux' in the file 'ERR009135.bam'.
I would love to know if it is a general R syntax error or is it a major error where I need to make modifications with my files such as the 'BAM' files (ERR009135.bam). Please do reply with any suggestions or modifications. Will be deeply appreciated.
Thank you in advance!
I am just starting to explore the rmarkdown package. I don't use Rstudio. I use the default R environment. What I did was as follows.
I created a new R document.
Started typing few lines in rmarkdown format.
Saved the file with Rmd extension.
I saved the file in the working directory.
I installed the pandoc using the pkg file.
I installed 'rmarkdown' package. Loaded the package.
Used the following command to render the Rmd file.
rmarkdown::render("Untitled.Rmd")
I get the following error.
Error in tools::file_path_as_absolute(input) : file 'Untitled.Rmd'
does not exist
I tried all the possible ways such as giving the exact path instead of filename etc. But nothing worked out. I googled the error message and found that none had similar error. Can someone help me with this. What I am missing. What the error message mean?
Most of the time the error file not found is either a type error or a real missing file (as in your case, the real one is named in another way).
In order to discard those possibilities:
Copy the fullpath from your filebrowser.
Make sure the file exists, inside R you could type:
file.exists("/fullpath/to/file")
If that return TRUE and the error persists, then you suspect another thing is going on.
I tried to load my R workspace and received this error:
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘WORKSPACE_Wedding_Weekend_September’ has magic number '#gets'
Use of save versions prior to 2 is deprecated
I'm not particularly interested in the technical details, but mostly in how I caused it and how I can prevent it in the future. Here's some notes on the situation:
I'm running R 2.15.1 on a MacBook Pro running Windows XP on a bootcamp partition.
There is something obviously wrong this workspace file, since it weighs in at only ~80kb while all my others are usually >10,000
Over the weekend I was running an external modeling program in R and storing its output to different objects. I ran several iterations of the model over the course of several days, eg output_Saturday <- call_model()
There is nothing special to the model output, its just a list with slots for betas, VC-matrices, model specification, etc.
I got that error when I accidentally used load() instead of source() or readRDS().
Also worth noting the following from a document by the R Core Team summarizing changes in versions of R after v3.5.0 (here):
R has new serialization format (version 3) which supports custom serialization of
ALTREP framework objects... Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0.
I encountered this issue when I saved a workspace in v3.6.0, and then shared the file with a colleague that was using v3.4.2. I was able to resolve the issue by adding "version=2" to my save function.
Assuming your file is named "myfile.ext"
If the file you're trying to load is not an R-script, for which you would use
source("myfile.ext")
you might try the readRDSfunction and assign it to a variable-name:
my.data <- readRDS("myfile.ext")
The magic number comes from UNIX-type systems where the first few bytes of a file held a marker indicating the file type.
This error indicates you are trying to load a non-valid file type into R. For some reason, R no longer recognizes this file as an R workspace file.
Install the readr package, then use library(readr).
It also occurs when you try to load() an rds object instead of using
object <- readRDS("object.rds")
I got the error when saved with saveRDS() rather than save(). E.g. save(iris, file="data/iris.RData")
This fixed the issue for me. I found this info here
Also note that with save() / load() the object is loaded in with the same name it is initially saved with (i.e you can't rename it until it's already loaded into the R environment under the name it had when you initially saved it).
I had this problem when I saved the Rdata file in an older version of R and then I tried to open in a new one. I solved by updating my R version to the newest.
If you are working with devtools try to save the files with:
devtools::use_data(x, internal = TRUE)
Then, delete all files saved previously.
From doc:
internal If FALSE, saves each object in individual .rda files in the data directory. These are available whenever the package is loaded. If
TRUE, stores all objects in a single R/sysdata.rda file. These objects
are only available within the package.
This error occured when I updated my R and R Studio versions and loaded files I created under my prior version. So I reinstalled my prior R version and everything worked as it should.