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@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@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@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.
Thanks!
Kind regards,
Roel Janssen
________________________________________
From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Sunday, July 23, 2017 7:44 PM
To: Vincent Carey; Janssen-10, R.R.E.
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Change in BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
Hi,
BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz was added to Bioconductor
in BioC 3.0 and has not changed since then. At least not on
master.bioconductor.org. These are the MD5 hashes of the tarball
for each version of BioC on master.bioconductor.org:
ubuntu@ip-172-30-4-20:/extra/www/bioc/packages$ md5sum
3.*/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.0/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.1/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.2/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.3/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.4/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.5/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
672a988b28d8602afb2bd5595db7303b
3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
Cheers,
H.
On 07/23/2017 04:31 AM, Vincent Carey wrote:
I can't reproduce this. Did you get
688,190,187
bytes in your tar.gz? Could it be an incomplete transfer?
On Sat, Jul 22, 2017 at 5:47 PM, Janssen-10, R.R.E. <
r.r.e.janssen...@umcutrecht.nl> wrote:
Hello,
It seems that the tarball BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz has
changed, without a change in version:
From
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_packages_release_data_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sS7Y9rGFRoKmYrCl4y_IWoYFjj7HImCxWm4hYXClAZc&s=_ruyoTPdHqKb8FyuBLOAVMyZk_8tT1Wc8evh6fGTY2Y&e=
annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz...
...SC.hg19_1.4.0.tar.gz 656.3MiB 5.6MiB/s 01:58 [####################]
100.0%
sha256 hash mismatch for output path `/gnu/store/
ml0l7hbplvnxssjcgbwzi8cnmcmnsypi-BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
expected: 0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2
actual: 1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8
What has changed here, and why hasn't the version number been updated
accordingly?
Kind regards,
Roel Janssen
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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