[Bioc-devel] Change in BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz

[Janssen-10, R.R.E.]

Hello Hervé,

> Hi,
> 
> On 07/30/2017 03:28 AM, Janssen-10, R.R.E. wrote:
>> Hello,
>>
>> So, are you absolutely sure nothing has changed in this package?
>
> All I'm saying it that version 1.4.0 of this package has not changed
> since it was first made on May 13, 2014. Before version 1.4.0, we had
> version 1.3.1000. Of course things have changed in the package between
> version 1.3.1000 and version 1.4.0. IIRC what changed is the way the
> chromosome sequences are stored on disk (in 2bit format since version
> 1.4.0, used to be something else).
> 
>> I can still reproduce the hash mismatch.
>>
>> In GNU Guix, the SHA256 hash is computed when the tarball is downloaded by the person who adds or changes the package. So at some point, the tarball was different (at least to to package maintainer).
> 
> Not necessarily. What if the original SHA256 hash got computed on a
> corrupted tarball?
> 
>>
>> The MD5 hashes you provided are the *current* hashes and does not say anything about the history of these files.
> 
> Note that they are the "current" hashes of tarballs that belong to
> versions of Bioconductor that have been frozen for years (every 6
> months we release a new BioC version and freeze the previous one).
> 
>> What is their last modification date?
> 
> webadmin at ip-172-30-4-20:/extra/www/bioc/packages$ ls -l
> 3.*/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 May 13  2014
> 3.0/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Apr 15  2015
> 3.1/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Oct 26  2015
> 3.2/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Oct 13  2015
> 3.3/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Oct 13  2015
> 3.4/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Oct 13  2015
> 3.5/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 webadmin webadmin 688190187 Oct 13  2015
> 3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> 
> Futhermore, all these tarballs are copies of a tarball I generated
> in 2014 on a server at the Fred Hutch called rhino3. I just went on
> this server and the original tarball is still there:
> 
>    hpages at rhino3:~/BSgenomeForge/forged/1.4.0$ ls -l
> BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> -rw-r--r-- 1 hpages g_hpages 688190187 May 13  2014
> BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> 
> As you can see, it's from May 13, 2014. Its M5 hash is:
> 
>    hpages at rhino3:~/BSgenomeForge/forged/1.4.0$ md5sum
> BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> 672a988b28d8602afb2bd5595db7303b  BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
> 
> Same hash as in my previous email.
> 
> I hope that's enough evidence that this tarball has never
> changed on our side.
> 
> Cheers,
> H.

Yes it is. Thanks!

Kind regards,
Roel Janssen
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