Installation Failure

[DarioS]

It can't find R.

   Error: package or namespace load failed for ‘DIFseq’ in dyn.load(file, DLLpath = DLLpath, ...):
    unable to load shared object '/tmp/Rtmp4fLz2P/Rinst28d78af008dd/00LOCK-DIFseq/00new/DIFseq/libs/DIFseq.so':
     /tmp/Rtmp4fLz2P/Rinst28d78af008dd/00LOCK-DIFseq/00new/DIFseq/libs/DIFseq.so: undefined symbol: gsl_sort_smallest_index
   Error: loading failed
   Execution halted
   ERROR: loading failed
─  removing ‘/tmp/Rtmp4fLz2P/Rinst28d78af008dd/DIFseq’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'DIFseq' from GitHub:
  ! System command 'R' failed

But, it is definitely in one of my PATH folders.

> system("Rscript")
Usage: Rscript [options] file [args]
   or: Rscript [options] -e expr [-e expr2 ...] [args]
A binary front-end to R, for use in scripting applications.
>
[1]+  Stopped                 R
~$ which R
/usr/sms/bin/R

My operating system is modern Debian.

~$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 12 (bookworm)
Release:        12
Codename:       bookworm

[songfd2018]

Dear Strbenac,

Thanks for your interest in our software! I am sorry for my late reply because I have been traveling three weeks and missed your message.

R packages should be installed in an R session as our installation guide ( https://github.com/songfd2018/DIFseq-Rpackage). In particular, run the following command in R console instead of command line

install_github("songfd2018/DIFseq-Rpackage")

What's your command to install DIFseq? Could you try to install DIFseq in R console?

Please feel free to let me know if you have any questions.

Best regards, Fangda

On Wed, Jun 12, 2024 at 8:00 AM Dario Strbenac @.***> wrote:

It can't find R.

Error: package or namespace load failed for ‘DIFseq’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/tmp/Rtmp4fLz2P/Rinst28d78af008dd/00LOCK-DIFseq/00new/DIFseq/libs/DIFseq.so': /tmp/Rtmp4fLz2P/Rinst28d78af008dd/00LOCK-DIFseq/00new/DIFseq/libs/DIFseq.so: undefined symbol: gsl_sort_smallest_index Error: loading failed Execution halted ERROR: loading failed ─ removing ‘/tmp/Rtmp4fLz2P/Rinst28d78af008dd/DIFseq’

ERROR: package installation failedError: Failed to install 'DIFseq' from GitHub: ! System command 'R' failed

But, it is definitely in one of my PATH folders.

system("Rscript") Usage: Rscript [options] file [args] or: Rscript [options] -e expr [-e expr2 ...] [args] A binary front-end to R, for use in scripting applications.> [1]+ Stopped R~$ which R /usr/sms/bin/R

My operating system is modern Debian.

~$ lsb_release -aNo LSB modules are available.Distributor ID: DebianDescription: Debian GNU/Linux 12 (bookworm)Release: 12Codename: bookworm

— Reply to this email directly, view it on GitHub https://github.com/songfd2018/DIFseq-Rpackage/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJHLKO6OGRBO6LX23YKRVBLZG6FSFAVCNFSM6AAAAABJFI4222VHI2DSMVQWIX3LMV43ASLTON2WKOZSGM2DONJQGAYDENA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Best regards, Fangda

[DarioS]

Installation was run as required in R console using install_github. I just showed the end of the process to highlight the error.

[songfd2018]

Hi Dario,

I am sorry that the current version only works on Windows. I am trying to handle the installation and complication issues on Linux. The current reason is that R fails to link the GSL library.

Thanks a lot for your patience!

Best regards, Fangda

On Wed, Jun 26, 2024 at 7:00 AM Dario Strbenac @.***> wrote:

Installation was run as required in R console using install_github. I just showed the end of the process to highlight the error.

— Reply to this email directly, view it on GitHub https://github.com/songfd2018/DIFseq-Rpackage/issues/1#issuecomment-2190142250, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJHLKO7NSUTWU4WU5OLSP6TZJHZBLAVCNFSM6AAAAABJFI4222VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJQGE2DEMRVGA . You are receiving this because you commented.Message ID: @.***>

-- Best regards, Fangda

[DarioS]

Ah, wonderful. I hope it is not too much effort to make installation work on Linux. Most research servers run Linux O.S.