File open mode error in R

Question

[dengziqi1234]

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.

require(rmotifx)
rmotifx

fg.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 former

bg.seqs = readLines(bg.path)

Warning message:
In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

head(fg.seqs)

character(0)

head(bg.seqs)

character(0)

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

[ecolonaut]

Can you edit your post to include your code scripts and the error you are getting in text format?

[dengziqi1234]

I'm sorry. I've edited it.

[WouterDeCoster]

I can't access that image (403 - Forbidden).

[dengziqi1234]

Sorry for that. Now i have written them out.

[WouterDeCoster]

I've modified your post using code formatting (the 101010 button).

Can you check the variables fg.path and bg.path and see if the file they point to really exists on your system?

[dengziqi1234]

Yes, they exists. I put them under the Working Directory.

[WouterDeCoster]

Actually, you don't have an error. Just warnings.

[cool.abbecker]

Please follow this guidelines: http://stackoverflow.com/help/how-to-ask http://stackoverflow.com/help/mcve

[WouterDeCoster]

Biostars also has a (probably similar) version of posting guidelines: How To Ask Good Questions On Technical And Scientific Forums

[cool.abbecker]

Sorry I am new and were not aware of the internal guidelines. I will link them next time. Thanks for the information!

[dengziqi1234]

Thank you for your information.

[dengziqi1234]

Thank you for information.

Answer 1

[ecolonaut]

I believe this is an issue with how you are calling your data, rather than something with the 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"

*EDIT: You'll need to find the files on your computer and change the path.

[dengziqi1234]

It make sense! Perfect! It works! Thank you very much, Mr.Gregory,I think.

[ddiez]

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 file(). That is, readLines("C:/Users/Gregory/Documents/R/win-library/3.3/rmotifx/extdata/fg-data-ck2.txt") should work just as fine.

Answer 2

[ddiez]

I believe the problem here is very different :-)

Looking for the 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"

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, motifx(), maintains its original name.

EDIT

The code in the README file has been fixed.

[dengziqi1234]

You are a attentive man! It works too! Thank you!