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

2017-07-30 Thread Hervé Pagès 

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

Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

2017-07-30 Thread Neumann, Steffen 
Hi, 

Hi,

any suggestions or better diagnostics that could help us 
fixing this, in case it really is something in xcms ? 

There were a few earlier reports with similar messages, 

back in 2013, slightly hinting at virus scanners: 
http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-output-file-quot-td4664111.html

Back in 2015, but both referring to SPB:
https://github.com/Bioconductor/packagebuilder/issues/2
https://github.com/Bioconductor/packagebuilder/issues/26

And from 2016 without any resolution:
https://github.com/r-hub/rhub/issues/58

Yours,
Steffen



On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> Dear all,
> 
> one of the xcms vignettes fails to build on tokay1 recently with the
> error message:
> 
> Warning: running command
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =
> engine) :
>   Failed to locate the 'texi2pdf' output file (by engine
> 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> 'new_functionality.R', 'new_functionality.Rmd',
> 'new_functionality.html', 'new_functionality.org', 'references.bib',
> 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 'xcmsMSn.Rnw',
> 'xcmsPreprocess.Rnw-notrun'
> Calls:  -> find_vignette_product
> Execution halted
> 
> is this some problem with tokay1 or is it related to the vignette (I
> have no problems building this vignette in my Windows build machine)?
> 
> thanks, jo
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
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IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] Change in BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz

2017-07-30 Thread Janssen-10, R.R.E. 
Hello,

So, are you absolutely sure nothing has changed in this package?
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).

The MD5 hashes you provided are the *current* hashes and does not say anything 
about the history of these files.
What is their last modification date?

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_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sS7Y9rGFRoKmYrCl4y_IWoYFjj7HImCxWm4hYXClAZc=_ruyoTPdHqKb8FyuBLOAVMyZk_8tT1Wc8evh6fGTY2Y=
>> 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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>
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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

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