problem with installation

[laurabuggiotti]

problem with installation

[fischuu]

Hi Laura,

sure, apparently you are trying to install hoardeR with an older R version, which results in some problems. However, unfortunately there are currently quite many dependencies in the package so that the installation might cause some problems anyway.

But what you can do, if you only aim for the subPhased() function, you can just source this function here from the github repository:

source("https://raw.githubusercontent.com/fischuu/hoardeR/master/R/subPhased.R")

there shouldn't be any further dependencies. After you have sourced that function it will be available for this session. If you need the fixed version of the function I would recommend to download the file instead, store it locally and then source it from your HDD.

Please let me know if this solves your issue or if you need any further help with it.

[laurabuggiotti]

Thanks for your prompt answer! Indeed the dependencies were mainly the problem, anyway I have now sourced the function. I used the following command to run it: subPhased(file="phased_file", vmmk = "Chr1-Variant-Map-Master-Key.txt", out="out_prova", chunkSize=100000, verbose=TRUE, removeInsertions=TRUE) but got the following message: I read the master key file Thu Feb 1 10:41:57 2018 Error in 1:nchunks : argomento NA/NaN do you reckon is something wrong with my file? Thanks a lot for your help, Laura 2018-01-31 17:18 GMT+00:00 Daniel Fischer <[email protected]>:

…

Hi Laura, sure, apparently you are trying to install hoardeR with an older R version, which results in some problems. However, unfortunately there are currently quite many dependencies in the package so that the installation might cause some problems anyway. But what you can do, if you only aim for the subPhased() function, you can just source this function here from the github repository: source("https://raw.githubusercontent.com/fischuu/ hoardeR/master/R/subPhased.R") there shouldn't be any further dependencies. After you have sourced that function it will be available for this session. If you need the fixed version of the function I would recommend to download the file instead, store it locally and then source it from your HDD. Please let me know if this solves your issue or if you need any further help with it. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Ah4mLbsb6-CZRhBHzCLQUBW0R9YeWqGwks5tQKBggaJpZM4R0P3t> .

[fischuu]

I just checked the code (I wrote it quite a while ago...), and I noticed that some of the codes are only work under Linux OS, so I would actually improve the function. Do you run it on Windows? I could prepare an OS safe version of it, but cannot do it today anymore (maybe in the evening, lets see).

I assume the issue is that I used back then a system command to determine the number of rows in the file, which is of course not the best way to do and should be fixed. Nowadays I would use the data.table package instead, I'll try to rewrite this part.

But if you know the number of lines inside your phased file, I could send you a quick fix...

Best wishes
Daniel

[laurabuggiotti]

im running it on OS (my macbook pro) but i could try to source the function in my user's environment of a cluster i have access to which has Linux. The number of lines are going to be different as i have phased genotypes by chromosomes (e-g chr1 number of lines 121819). Thanks, Laura 2018-02-01 11:18 GMT+00:00 Daniel Fischer <[email protected]>:

…

I just checked the code (I wrote it quite a while ago...), and I noticed that some of the codes are only work under Linux OS, so I would actually improve the function. Do you run it on Windows? I could prepare an OS safe version of it, but cannot do it today anymore (maybe in the evening, lets see). I assume the issue is that I used back then a system command to determine the number of rows in the file, which is of course not the best way to do and should be fixed. Nowadays I would use the data.table package instead, I'll try to rewrite this part. But if you know the number of lines inside your phased file, I could send you a quick fix... Best wishes Daniel — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Ah4mLY2QE-Oa-BEWYnTHFMRyqvoBmh-zks5tQZ2JgaJpZM4R0P3t> .

[fischuu]

I just changed the part that determines the number of lines, maybe that helps to run the function, though it might be slow. I really should change that function to use the data table package, I try to do that asap, but currently I do not have test data with me, so it might take until Monday...

In the meanwhile, you could try to source this fix here:

source("https://raw.githubusercontent.com/fischuu/hoardeR/master/R/subPhased_uglyFix.R")

[laurabuggiotti]

Hi Daniel, it works fine in the cluster! Thanks a lot for your help, Laura 2018-02-01 11:24 GMT+00:00 laura buggiotti <[email protected]>:

…

im running it on OS (my macbook pro) but i could try to source the function in my user's environment of a cluster i have access to which has Linux. The number of lines are going to be different as i have phased genotypes by chromosomes (e-g chr1 number of lines 121819). Thanks, Laura 2018-02-01 11:18 GMT+00:00 Daniel Fischer ***@***.***>: > I just checked the code (I wrote it quite a while ago...), and I noticed > that some of the codes are only work under Linux OS, so I would actually > improve the function. Do you run it on Windows? I could prepare an OS safe > version of it, but cannot do it today anymore (maybe in the evening, lets > see). > > I assume the issue is that I used back then a system command to determine > the number of rows in the file, which is of course not the best way to do > and should be fixed. Nowadays I would use the data.table package instead, > I'll try to rewrite this part. > > But if you know the number of lines inside your phased file, I could send > you a quick fix... > > Best wishes > Daniel > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#5 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/Ah4mLY2QE-Oa-BEWYnTHFMRyqvoBmh-zks5tQZ2JgaJpZM4R0P3t> > . >

[fischuu]

Okay, perfect! Hopefully it will serve you well then!

but for future reference I should really change it to get it OS independent...

Best wishes,
Daniel