some errors for Makefile
Closed this issue · 6 comments
I observe that the Makefile file was recently updated, but I encountered an error with no rules to make the target, causing the make execution to stop.
There are no rules for making the target “share/seqrequester/ultra-long-nanopore”，由“/home/bio-3090ti/Benz_code/GNNome-assembly/vendor/seqrequester/build/share/seqrequester/ultra-long-nanopore” requirements. Stop.
A fresh clone built fine for me with GNU Make 4.3. Which version are you using?
The source of the file it is trying to install is ..../vendor/seqrequester/share/ultra-long-nanopore; does that file exist?
The error message is unfamiliar. If I remove that file and try building, I get:
gmake: *** No rule to make target '../share/ultra-long-nanopore', needed by '/scratch/seqrequester/build/share/seqrequester/ultra-long-nanopore'. Stop.
which is worded differently, but more importantly, the target path is quite different.
A fresh clone built fine for me with GNU Make 4.3. Which version are you using?
The source of the file it is trying to install is
..../vendor/seqrequester/share/ultra-long-nanopore; does that file exist?The error message is unfamiliar. If I remove that file and try building, I get:
gmake: *** No rule to make target '../share/ultra-long-nanopore', needed by '/scratch/seqrequester/build/share/seqrequester/ultra-long-nanopore'. Stop.which is worded differently, but more importantly, the target path is quite different.
Thank you for your reply. I used GNU Make 4.2.1. Should i update my Make? And Yes, ultra-long-nanopore is already exists, should I remove it and reinstall it, or has it been stated that I have installed successfully. Beside. I found it under the path "../seqrequester/build/bin/seqrequester", Is this proof that I finished the seqrequester installation? Thanks again
And I've noticed there seems to be a difference in our paths
share/seqrequester/ultra-long-nanopore its me
seqrequester/share/ultra-long-nanopore its your
Is it because the path is reversed that ultra-long-nanopore can't find it？But I didn't change the Makefile.
if yes, Although this sounds simple, I am not familiar with the syntax of cmake. So I need you to help me check, thank you !~
I'm not sure what's going wrong here. If you have these four files, it installed correctly:
> ls -l build/share/seqrequester/* build/bin/seqrequester
-rwxr-xr-x 1 bri bri 2417928 Jun 24 10:48 build/bin/seqrequester
-rw-r--r-- 1 bri bri 1139703 Jun 24 09:31 build/share/seqrequester/pacbio
-rw-r--r-- 1 bri bri 97398 Jun 24 09:31 build/share/seqrequester/pacbio-hifi
-rw-r--r-- 1 bri bri 2040814 Jun 24 09:31 build/share/seqrequester/ultra-long-nanopore
(The size of 'seqrequester' will be different.) I suspect you're missing the last three, but you can install manually:
cp share/* build/share/seqrequester/
u are right. I have this file build/bin/seqrequester, but dont have others. So i used u solution. cp share/* build/share/seqrequester/, and i find other 3 file in same path sa u. So I guess I'm done with the installation. Since I didn't download the dataset I just run /seqrequester/build/bin/seqrequester, I received the following output:
usage: /home/bio-3090ti/Benz_code/GNNome-assembly/vendor/seqrequester/build/bin/seqrequester [mode] [options] [sequence_file ...]
MODES:
summarize report N50, length histogram, mono-, di- and tri-nucleotide frequencies
extract extract the specified sequences
sample emit existing sequences randomly
generate generate random sequences
microsatellite compute microsatellite percent per window size
simulate errors in existing sequences
ERROR: No mode (summarize, extract, generate, et cetera) specified.
ERROR: Supplied options don't make sense.
I think I'm done with the installation. Thank u very much~I'll run it on the instance as much as possible
I finally figured out this problem. Cheers!