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Runtime errors about buffer overflows #63
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Hi @Y4NG333 , Sorry for the late response. Github didn't send me an e-mail for this issue, i will go after this. No, I haven't seen such an error before. Could you:
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Thank you! I suspect conversion did something weird. The error presumably takes places reading your compressed file. If there are no legal issues regarding your test file, would you mind sendin me an e-mail with the plain test fasta and the fastafs archive ( Thank you so much for reporting. |
OK, it's been emailed to you. |
Thanks @Y4NG333, I received your e-mail. During the day I will be doing non-fastafs releated data analysis. I will try to make time for this soon after! |
OK, thanks a lot! |
Hi @Y4NG333 , I've been testing but I can't reproduce it. Your files are byte identical to mine, so it must be the fastafs binary behaving differently on your system than on mine. Which git commit did you compile ( Could you run Youri |
Thanks @yhoogstrate , When I run make check command, it shows that there is a problem with a part of the test, as shown in the following figure: I downloaded the code to my linux system through the git clone command, and then followed the readme file: |
This is interesting. Could you copy the output of I suspect there is something going wrong with integer conversion or something. I will probably make a branch with all kind of debug messages, ask you to re-compile and copy the output of test again. |
OK, thanks a lot! I sent the file to your email. |
@Y4NG333 Could you also send me he output when running those binaries directly from the command line ($ |
Hi again, My appologies for all this disturbance. I have created a branch with more debug options for me. Could you do the following from the main fastafs directory:
Please send me the debug messages. If you know how to use gdb, could you please run this? and copy all the uitput after |
The specific debugging information has been sent to you, thank you very much for your help. |
Oh no, thank you!! Are you running ubuntu 21.04 or 21.10? I will also setup a VM. |
Thanks. I found a compile bug for 21.10 and resolved it. Could you run:
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What!? and without piping the output to the debug-messages file? juist |
When I enter the code ./bin/test/test_fastafs, the file is as follows: (Because the content is too long, I can't take a screenshot, I will send you a copy of the entire file) |
I am totally lost. The code only contains additional printing messages and somehow it now works. |
Hi @Y4NG333, I haven't received an update from you anymore. Did you get the master branch working without issues? Youri |
Hi again, Hmm, if the debug branch never errors out and the main branch does, I honestly don't know/understand what is causing this.
Otherwise maybe we need to do a teams or zoom session? |
Found it, checking the version of FASTAFS or UCSC 2bit went 4 bytes out of bound. Thanks @Y4NG333 . Finally I could reproduce it because of your bug report!!! I found it by usingVMs of other distro's. |
Hello, after compiling according to the readme file, when I run the fastafs list command, there is a problem of detecting buffer overflow. Have you encountered this situation? If this happens, how to solve this problem? Thank you very much.
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