Installation error with the latest version of sequenza

[Fenisha Shah]

Hello 

I had teh sequenza.3.00 installed and persistently kept getting this error: 
Error in (function (x, col_types)  : unused argument (parallel = 1)

when I ran sequenza.extract. I tried to pull the new sequenza package from the bitbucket: 
git clone -b chemins https://bitbucket.org/sequenzatools/sequenza.git

After installing all the relevant dependencies when I try to install this package I get the error in below. I have tried R version 3.6.3 and 4.2.3 and I get the same error in both the versions: 

* installing *source* package ‘sequenza’ ...

** using staged installation

** libs

make: Nothing to be done for 'all'.

installing to /PHShome/fs740/.conda/envs/my_r_env/lib/R/library/00LOCK-sequenza/00new/sequenza/libs

** R

Error in parse(outFile) : 

  /data/gulhanlab/Fenisha/sequenza/R/windows.R:86:0: unexpected end of input

84:   })

85: }

   ^

ERROR: unable to collate and parse R files for package ‘sequenza’

* removing ‘/PHShome/fs740/.conda/envs/my_r_env/lib/R/library/sequenza’

Warning message:

In install.packages("/data/gulhanlab/Fenisha/sequenza", repos = NULL,  :

  installation of package ‘/data/gulhanlab/Fenisha/sequenza’ had non-zero exit status

Can you please provide some guidance on solving this issue. 

Best,

Fenisha

[favero.f...@gmail.com]

Hi Fenisha,

this is odd, do you have the same behaviour if you install it with devtools::install_bitbucket?

best

Francesco

from iPhone

Il giorno 27 giu 2024, alle ore 00:40, 'Fenisha Shah' via Sequenza User Group <sequenza-...@googlegroups.com> ha scritto:

Hello 

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[Fenisha Shah]

Hello Francesco

That seems to work! Thank you for your prompt response. I would like to highlight another problem. I saw there was somebody else to had the same error when using the extract function in sequenza to generate the segment txt files. Do you have any recommendations on this? 

> test <- sequenza.extract(data.file, verbose = FALSE)

Error: upper value must be greater than lower value 

Best,

Fenisha