unable to checkout / compile

[proukakis]

Describe the bug cannot checkout from git

To Reproduce git clone https://github.com/mills-lab/PALMER.git Cloning into 'PALMER'... remote: Enumerating objects: 27, done. remote: Counting objects: 100% (27/27), done. remote: Compressing objects: 100% (25/25), done. remote: Total 610 (delta 9), reused 0 (delta 0), pack-reused 583 Receiving objects: 100% (610/610), 74.39 MiB | 10.85 MiB/s, done. Resolving deltas: 100% (293/293), done. git-lfs smudge 'index/Alu.regions.GRCh37': git-lfs: command not found error: external filter git-lfs smudge %f failed -1 error: external filter git-lfs smudge %f failed fatal: index/Alu.regions.GRCh37: smudge filter lfs failed warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry the checkout with 'git checkout -f HEAD'

Then trying to unzip directory

and use make as below (or owthout specifying compilers)

make CC=gcc-6 CXX=g++-6 rm -f PALMER g++ -o PALMER PALMER.v1.4.cpp

PALMER.v1.4.cpp:396:20: error: variable length array of non-POD element type 'string' (aka 'basic_string<char, char_traits, allocator >') string chr_inde[line_chr]; ^ 1 error generated. make: *** [PALMER] Error 1

Additional context Please note I am using Mac OS. Perhaps this is the problem, but i still don't understand why the git clone would fail. I have access to Linux if you think this will fix it.

thanks christos

[WeichenZhou]

Hi Christos, Thanks for your posting. Could you please check the directory /PALMER/index to see whether there are files downloaded (MB size level)? If not, I think ONE reason would be you need git-lfs to download all files. I will re-upload the files and make sure the downloading does not require lfs anymore. If you have successfully downloaded all files (including index files) and still have the same problem, please let me know.

Thanks Arthur

[proukakis]

yes, the index files are not there, sounds like this is the problem, thanks

[WeichenZhou]

You might wanna try to install git-lfs to download the full package and immediately use PALMER. In the meantime, I will update the files ASAP. Thanks!!

[proukakis]

Yes will do tomorrow, Thanks

Sent from my iPhone so please forgive brevity and any errors

---

From: Weichen (Arthur) Zhou notifications@github.com Sent: Tuesday, October 22, 2019 7:13:40 PM To: WeichenZhou/PALMER PALMER@noreply.github.com Cc: Proukakis, Christos c.proukakis@ucl.ac.uk; Author author@noreply.github.com Subject: Re: [WeichenZhou/PALMER] unable to checkout / compile (#13)

You might wanna try to install git-lfs to download the full package and immediately use PALMER. In the meantime, I will update the files ASAP. Thanks!!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/WeichenZhou/PALMER/issues/13?email_source=notifications&email_token=AENBYSFAG4DZCXWVVJC3YQTQP47FJA5CNFSM4JDNE7W2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB6WAUY#issuecomment-545087571, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AENBYSD2PY4QZMN2C2XSRHTQP47FJANCNFSM4JDNE7WQ.

[WeichenZhou]

Close this issue.

[proukakis]

hello, i know this is closed, but i tried the install just now on mac with the latest version and it seems to work!

[WeichenZhou]

Thanks.