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Re: [MoM] bcalm package



Hi Shayan,

On Thu, Sep 26, 2019 at 07:47:18PM +0100, Shayan Doust wrote:
> I believe bcalm[1] is done. Hopefully not missing any dependency.

Thanks for working on this.  Build-Depends cmake was missing - fixed.

...
Gluing partition 140 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 160 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 180 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 200 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 220 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 240 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 260 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 280 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 300 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 320 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 340 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 360 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 380 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 400 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 420 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 440 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 460 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 480 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Gluing partition 500 (size: 0 MB)               06:51:22     memory [current, maxRSS]: [  51,   98] MB 
end                                             06:51:22     memory [current, maxRSS]: [  51,   98] MB 
debug: not deleting glue files
Finding links between unitigs                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 0                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 1                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 2                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 3                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 4                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (2kmers/2extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 5                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 6                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 1 pass 7                                   06:51:22     memory [current, maxRSS]: [  51,   98] MB 
step 2 (0kmers/0extremities)                    06:51:22     memory [current, maxRSS]: [  51,   98] MB 
gathering links from disk                       06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Done finding links between unitigs              06:51:22     memory [current, maxRSS]: [  51,   98] MB 
Traceback (most recent call last):
  File "compare_fasta.py", line 20, in <module>
    s1 = read_seqs(fasta1)
  File "compare_fasta.py", line 15, in read_seqs
    for  line in open(fasta):
  File "/usr/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
test KO
autopkgtest [06:51:22]: test run-unit-test: -----------------------]
autopkgtest [06:51:22]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 1
autopkgtest [06:51:22]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test        FAIL non-zero exit status 1


I have forced "export LC_ALL=C.UTF-8" in run-unit-tests - but this does not change anything
(BTW, that's my most hatet Python error message - I've seen it sooooo frequently :-( )
 
> I also believe FAST is in the pipeline to upload seeing how some issues
> were rectified with fonts.

Ahhh, well, you had

commit 77ff787eb810742eac574d1a9439f5dbe62acec3
Author: Shayan Doust <hello@shayandoust.me>
Date:   Sun Sep 22 23:41:24 2019 +0100

    Patch to eliminate the need for contrib fonts package

and I even have a local commit "Upload to new" - but this never
happened.  I've probably build it at home and forgot to dput.  Thanks
for the ping.  It might happen that my network connection is to weak to
upload before Sunday evening or Monday.  Sorry for the delay - please
ping again if you do not see anything until Tuesday.

> I also want to personally refrain from
> anymore new packages for a while because bugs list needs some attention
> which I will certainly give it overall.

Perfectly fine.  Any contribution is more than welcome - there is no
priotity of adding new packages over enhancing the quality of the
existing ones.

Thanks a lot for your work as always

       Andreas.
 
> [1]: https://salsa.debian.org/med-team/bcalm


-- 
http://fam-tille.de


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