File open mode error in R 1 Entering edit mode 7.4 years ago dengziqi1234 ▴ 20 Hello!I'm using a package from github. I've installed it. But when i follow the guideline. I met a error about opening file. Those two file are peptide sequence file. So i need to readLines them. I'm wondering how can i fix it?Thank you! here's the original tutorial: https://github.com/omarwagih/rmotifx R data analysis alignment • 4.7k views ADD COMMENT • link updated 7.4 years ago by ddiez ★ 2.0k • written 7.4 years ago by dengziqi1234 ▴ 20 1 Entering edit mode Can you edit your post to include your code scripts and the error you are getting in text format? ADD REPLY • link 7.4 years ago by ecolonaut ▴ 100 1 Entering edit mode I'm sorry. I've edited it. ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 Entering edit mode I can't access that image (403 - Forbidden). ADD REPLY • link 7.4 years ago by WouterDeCoster 47k Entering edit mode Sorry for that. Now i have written them out. ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 Entering edit mode I've modified your post using code formatting (the Can you check the variables ADD REPLY • link 7.4 years ago by WouterDeCoster 47k Entering edit mode Please follow this guidelines:http://stackoverflow.com/help/how-to-askhttp://stackoverflow.com/help/mcve ADD REPLY • link 7.4 years ago by cool.abbecker ▴ 30 Entering edit mode Biostars also has a (probably similar) version of posting guidelines: How To Ask Good Questions On Technical And Scientific Forums ADD REPLY • link 7.4 years ago by WouterDeCoster 47k Entering edit mode Sorry I am new and were not aware of the internal guidelines. I will link them next time. Thanks for the information! ADD REPLY • link 7.4 years ago by cool.abbecker ▴ 30 Entering edit mode Thank you for your information. ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 Entering edit mode Thank you for information. ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 4 Entering edit mode 7.4 years ago ecolonaut ▴ 100 I believe this is an issue with how you are calling your data, rather than something with the *EDIT: You'll need to find the files on your computer and change the path. ADD COMMENT • link 7.4 years ago by ecolonaut ▴ 100 Entering edit mode It make sense! Perfect! It works! Thank you very much, Mr.Gregory,I think. ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 Entering edit mode Just a small comment. If you pass the entire path with the filenames as a string, you don't need them to go with a call to ADD REPLY • link 7.4 years ago by ddiez ★ 2.0k 4 Entering edit mode 7.4 years ago ddiez ★ 2.0k I believe the problem here is very different :-) Looking for the So you have to change the parts that refer to motifx for rmotifx. My guess is, the package was once called motifx and the examples on the README file where written then. Later, the package was renamed as rmotifx but the documentation was not updated. Interestingly, the main function, EDIT The code in the README file has been fixed. ADD COMMENT • link 7.4 years ago by ddiez ★ 2.0k Entering edit mode You are a attentive man! It works too! Thank you! ADD REPLY • link 7.4 years ago by dengziqi1234 ▴ 20 require(rmotifx)rmotifxfg.path = system.file("extdata", "fg-data-ck2.txt", package="motifx")bg.path = system.file("extdata", "bg-data-serine.txt", package="motifx")fg.seqs = readLines(fg.path)Warning message:In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the formerbg.seqs = readLines(bg.path)Warning message:In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the formerhead(fg.seqs)character(0)head(bg.seqs)character(0)
101010
button).fg.path
and bg.path
and see if the file they point to really exists on your system?readLines()
function. After trying the example on my console I got the same error. The system.files()
calls don't work so the objects bg.path
and fg.path
are empty, and when readLines()
tries to search for the .txt files it can't find them. So, you just have to tell R exactly where to find the files you want it to run. You can do this by just including the entire file path in the readLines()
call:fg.seqs = readLines(file("C:/Users/Gregory/Documents/R/win-library/3.3/rmotifx/extdata/fg-data-ck2.txt"))bg.seqs = readLines(file("C:/Users/Gregory/Documents/R/win-library/3.3/rmotifx/extdata/bg-data-serine.txt")) head(fg.seqs)###[1] "KRAGGEESQFEMDI_" "SSYGISETTLEEIFL" "SYGISETTLEEIFLK"###[4] "FLKVAEESGVDAETS" "WSLNKEDTSEQVVPV" "KKLSVPTSDEEDEVP"
file()
. That is, readLines("C:/Users/Gregory/Documents/R/win-library/3.3/rmotifx/extdata/fg-data-ck2.txt")
should work just as fine.motifx
package (why? because I didn't read the entire question at first, just the call to system.file()
...) I found the following github page. In the README file there is an example exactly like the one the OP includes. If I run that example, I get the same error. However, there is an important detail: This R package is not named motifx, but rmotifx! If you consider that fact an run the following code, everything works as expected:system.file("extdata", "fg-data-ck2.txt", package="rmotifx")[1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rmotifx/extdata/fg-data-ck2.txt"
motifx()
, maintains its original name.
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