I am dealing with fonts in R for the first time. I have tried every solution I could find on stack and elsewhere to get fonts into R for me, but thus far I have had no success. At the most basic level, this is what I am trying to do:
install.packages('extrafonts')
library(extrafonts)
font_import()
At that point, I run into a big mess that I'm not really understanding well. My console shows me that first R is scanning ttf files, then extracting .afm files from .ttf files, and then it repeatedly references these long file extensions followed by ": No FontName. Skipping."
A full piece of the error message looks like this:
/System/Library/Fonts/Supplemental/Arial Unicode.ttfsh: line 1: 39188 Segmentation fault: 11 '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Unicode.ttf' '/var/folders/3h/yfpgl52j7rbb5l68lrwdvv_m0000gn/T//RtmpgwAvQc/fonts/Arial Unicode' 2>&1
: No FontName. Skipping.
Does anyone have any idea exactly what is going on here?
I know that the fonts aren't importing because when I run loadfonts() followed by fonts() or fontstable(), I get NULL. And when I try to pull a font other than the three native families in R into the theme of my ggplot function, the plot doesn't generate.
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.)
I am currently attempting to use R to read a (large, 8.3 MB) .xlsx file into a matrix. I am attempting to do so with the read.xlsx file in the xlsx package. https://cran.r-project.org/web/packages/xlsx/index.html
I am now trying to read the contents of one of the sheets in the file with the following command:
sheetname<-read.xlsx("/Users/jinkinsonsmith/Downloads/Re _Introduction/filename.xlsx",sheetName='sheetname')
It looks like this command should work in terms of reading the contents of sheet "sheetname" in xlsx file "filename" into the vector "sheetname". However, instead, I am getting this error message:
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod",
cl, : java.lang.OutOfMemoryError: Java heap space
It seems like I'm not the first person to get this error message (example: How to deal with "java.lang.OutOfMemoryError: Java heap space" error?), but even after reading the other post I just linked it is still not clear to me what I should do to fix this error. My MacBook Pro has long had issues with running out of disk space and requiring me to delete a bunch of files, so that could be the culprit, but it is also apparently possible that I have too many stored references to objects in R that I no longer use and that are taking up too much space. In the latter case I don't know how I would remove any unneeded references.
By using the following line of code before you load any other package, I could solve similar problems like this. I already described it here.
options(java.parameters = c("-XX:+UseConcMarkSweepGC", "-Xmx8192m"))
library(xlsx)
Please add this line and restart, since other packages can load some java things by themselves and the options have to be set before any Java is loaded.
In general, these option change the type of garbage collection which sometimes makes problems in the default settings and also increases the memory to 8GB.
I am trying to import fonts for ggplot2 graphs as in described here at work and it does not function (I succeeded easily at home).
Whether I try to do all fonts at the same time,
font_import()
y
Or font by font (amusingly, they are displayed by default by windows in a different case than how they are actually stored) :
font_import(pattern = "arial.ttf")
y
I get the following error message :
Scanning ttf files in C:\windows\Fonts ...
Extracting .afm files from .ttf files...
C:\Windows\Fonts\ahronbd.ttfError in system2(ttf2pt1, c(args, shQuote(ttfiles[i]), shQuote(tmpfiles[i])), :
'CreateProcess' failed to run 'C:\Users\name\DOCUME~1\R\WIN-LI~1\3.6\Rttf2pt1\exec\ttf2pt1.exe -a -G fAe "C:\Windows\Fonts\ahronbd.ttf" "C:\Users\name\AppData\Local\Temp\RtmpCyAu4H/fonts/ahronbd"'
And I have not found anything particularly helpful on the matter.
One reason might be speceific restrictions set by the IT at me company, but I am unsure where to start.
Is there a relatively simple way to see at what point the process is stopping ?
If not, would it be doable to copy/paste fonts "by hand", but then where am I supposed to paste what ?
I have checked that I have indeed the Arial font :
I am attempting to automate the insertion of JPEG images into Powerpoint. I have a macro done for that already, except using R would be infinitely better for my purposes.
The package R2PPT should do this, I understand. However, I cannot use it. For example, when I try to use PPT.Open, I understand I can do it two different ways by calling method = "rcom" or method = "RDCOMClient". Using the latter, R will always crash, sending an error report to windows. Using the former, it tells me I need to install statconnDCOM , before giving the error:
Error in PPT.Open(x) : attempt to apply non-function.
I cannot install statconnDCOM freely, as I wouldn't call this work non-commercial. So if there isn't a way to get around this issue, are there at least some free alternatives to R2PPT so that I can save several hours of manual work with a simple R code? If there is a way for me to use R2PPT, that would be ideal.
Thanks!
Edit:
I'm using R version 2.15 and downloaded the most recent version of R2PPT. Powerpoint is 2007.
Do you have administrative privileges on this machine?
There is an issue with package RDCOMClient. It needs permissions to write file rdcom.err in the root of drive C:. If you don't have privileges to write to c:, there is a rather cumbersome workaround:
Close R
Create "c:\temp" folder if it doesn't exist.
Locate on your hard drive file rdcomclient.dll. It usually placed in \R\library\RDCOMClient\libs\i386\ and in \R\library\RDCOMClient\libs\x64\ (you need to patch file which corresponds your Windows version - 32 bit or 64 bit). It's recommended to make backup copy of this files before patching.
Open rdcomclient.dll in text editor (Notepad++, for example -http://notepad-plus-plus.org/)
Find in file string c:\rdcom.err - it occurs only once.
Go into overwrite mode (usually by pressing "Ins" key). It is very important that new path will have the same number of characters as original one. Type C:\temp\e.rr instead of c:\rdcom.err
Save the file.
Now all should work fine.
Arguably not an answer, but have you looked at using Sweave/knitr to render your presentations in LaTeX using something like Beamer? (As discussed on slide 17 here.)
Wouldn't help any with getting JPGs into a PowerPoint, but would certainly make putting R-output (numerical or graphical) into a presentation much easier!
Edit: if you want to use knitr (which I recommend), here's another reference.
I want to find the location of the script .R files which are used for computation in R.
I know that by typing the object function, I will get the code which is running and then I can copy and edit and save it as a new script file and use that.
The reason for asking to find the foo.R file is
Curiosity
Know what is the algorithm used in the numerical computations
More immedietly, the function from stats package I am using, is running results for two of the arguments and not the others and have to figure out how to make it work.
Error shown by R implies that there might be some modification required in the script file.
I am looking for a more general answer, if its possible.
Edit: As per the comments so far, here is the code to compute spectrum of a time series using autoregressive methods. The data input is a univariate series.
x = ts(data)
spec.ar(x, method = "yule-walker") 1
spec.ar(x, method = "burg") 2
command 1 is running ok.
command 2 gives the following error.
Error in ar.burg.default(x, aic = aic, order.max = order.max, na.action = na.action, :
Burg's algorithm only implemented for univariate series
I did try specify all the arguments correctly like na.action=na.fail, order.max = NULL etc but the message is the same.
Kindly suggest possible solutions.
P.S. (This question is posted after searching the library folder where R is installed and zip files which come with packages, manuals, and opening .rdb, .rdx files)
See FAQ 7.40 How do I access the source code for a function?
In most cases, typing the name of the function will print its source
code. However, code is sometimes hidden in a namespace, or compiled.
For a complete overview on how to access source code, see Uwe Ligges
(2006), “Help Desk: Accessing the sources”, R News, 6/4, 43–45
(http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf).
When R installs a package, it evaluates all the ".R" source files and re-saves them into a binary format for faster loading. Therefore you typically cannot easily find the source file.
As has been suggested elsewhere, you can simply type the function name and see the source code, or download the source package and find the source there.
library(plyr)
ddply # prints the source for ddply
# See the content of the R directory for plyr,
# but it's only binary files:
dir(file.path(find.package("plyr"), "R"))
# [1] "plyr" "plyr.rdb" "plyr.rdx"
# Get the source for the package:
download.packages("plyr", "~", type="source")
# ...then unpack and inspect the R directory...
.libPaths() should tell you all of your current library locations. It's possible to have more than one installation of a package if there are two libraries but only the one that is in the first library will be used. Unless you offer the code and the exact error message, it's not likely that anyone will be able to offer better advice.
I think you are asking to see what I call the source code for a function in a package. If so, the way I do it is as follows, which has worked successfully for me on the three times I have tried. I keep these instructions handy in a few places and just copied and pasted them here:
To see the source code for a function in Program R download the package containing the function. Specifically, download the file that ends in "tar.gz". This is a compressed file. Expand the compressed file using, for example, "WinZip". Now you need to open the uncompressed file that ends in ".tar". Download the free software "7-Zip". Click on the file "7zFM.exe" and navigate to the directory containing the ".tar" file. You can extract the contents of that ".tar" file into a new folder. The contents consist of R files showing the source code for the functions in the R package.
EDIT:
Today (July 8, 2012) I was able to open the 'tar.gz' file using the latest version of 'WinZIP' and could copy the contents (the source code) from there without having to use '7-Zip'.
EDIT:
Today (January 19, 2013) I viewed the source code for functions in base R by downloading the file
'R-2.15.2.tar.gz'
To download that file go to the http://cran.at.r-project.org/ webpage and click on that file in this line:
"The latest release (2012-10-26, Trick or Treat): R-2.15.2.tar.gz, read what's new in the latest version."
Unzip the file. WinZip will work, or it did for me. Then search your computer for readtable.r or another base R function.
agstudy noted here https://stackoverflow.com/questions/14417214/source-file-for-r-function that source code for read.csv is located in the file readtable.r, so do not expect every base R function to have its own file.