Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2016-10-17 Thread Ramon Diaz-Uriarte 
Thanks Hervé.

R.


On Mon, 17-10-2016, at 11:32, Hervé Pagès  wrote:
> Hi Ramon,
>
> Yes the issue is known. The vsn maintainers have fixed the problem
> yesterday in svn, right before the builds started. All the failures
> due to vsn not installing on the build machines should be gone in
> today's report.
>
> Cheers,
> H.
>
> On 10/17/2016 01:34 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now
>> (last 24 to 48 hours?) failing to build in BioC 3.4 in Linux (malbec1) and
>> Mac OSX (morelia). Looking at the error reports they seem to be due to vsn
>> not being available. Checking the vsn report
>> (http://bioconductor.org/checkResults/3.4/bioc-LATEST/vsn) it seems vsn
>> required R-3.4.0 at the time of the check. However, the new vsn on the svn
>> repo (v.3.41.8) has
>>
>> Depends: R (>= 3.0.0), Biobase
>>
>>
>> So I guess we just need to wait for vsn to be rebuilt? I would normally
>> just wait quietly, but I am concerned because I think the creation of the
>> BioC 3.4 release branch is today and release is tomorrow.
>>
>> Best and apologies for the noise if this issue is known,
>>
>>
>> R.
>>
>>
>>


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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[Bioc-devel] 3.4 branch created in svn

2016-10-17 Thread Hervé Pagès 

The BioC 3.4 branch is now ready.

Remember, you always have access to 2 versions of your package in svn:
the "release" and "devel" versions.

Right now the "release" version of your package (which is
not officially released yet but will be tomorrow if
everything goes well) is in the 3.4 branch and accessible at:


https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/

Only bug fixes and documentation improvements should go here.

As always the "devel" version of your package is at:

  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/

Normal development of your package can resume here.

Similarly for experiment packages, where the "release" version of your
package is at:


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/

and the "devel" version at:

  https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

Please let us know if you have any questions.

Thanks,
H.

--
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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[Bioc-devel] Bioconductor 3.4 branch to be created in about 1 hour - do not commit during this time

2016-10-17 Thread Hervé Pagès 

Hello BioC developers,

We will be creating the Bioconductor 3.4 branch today in about one hour
(around 2:30pm EST).

Please stop all commits to trunk before 2:30pm EST (18:30 UTC) and do
not resume until further notice.

We will send another email when it is OK to resume commits. The
process (once it starts) should not take more than an hour.

Thanks!

H.

--
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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Re: [Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

2016-10-17 Thread zhao shilin 
Thanks Hervé!

2016-10-17 2:18 GMT-05:00 Hervé Pagès :

> Hi Shilin,
>
> I answered this on the support site:
>
>   https://support.bioconductor.org/p/88232/#88347
>
> Cheers,
> H.
>
>
> On 10/16/2016 08:35 PM, zhao shilin wrote:
>
>> Dear BioC team,
>>
>> I think I found something incorrect in  TxDb.Hsapiens.UCSC.hg38.knownG
>> ene,
>> and reported in https://support.bioconductor.org/p/88232/ but didn't get
>> reply. I think it is a bug, so decided to send it via email to let you
>> know.
>>
>> I am using the developing version of TxDb.Hsapiens.UCSC.hg38.knownGene,
>> because the release version is build in 2015 and has a lot of difference
>> with UCSC website. Here is the R code for the bug:
>>
>> require(TxDb.Hsapiens.UCSC.hg38.knownGene)
>> require(GenomicRanges)
>>
>> geneDb=TxDb.Hsapiens.UCSC.hg38.knownGene
>> allGeneRange<-genes(geneDb)
>> allGeneRange["875"]
>> txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg38.knownGene)
>> txs["875"]
>>
>>
>> We can find CBS gene (txs["875"]) has 25 transcripts, from two
>> regions: chr21   [6444869, 6467509] and chr21 [43075107, 43076288]
>>
>> 1. CBS gene ("875") was only in chr21 [43075107, 43076288]. The region
>> of chr21   [6444869, 6467509] was CBSL gene ("102724560"). But CBSL was
>> not
>> in the database, and its transcripts were recorded in CBS.
>>
>> 2. The gene region of CBS gene (allGeneRange["875"]) was in chr21
>> [6444869,
>> 43076943], which included all the region between 6444869-43076943. But it
>> is not correct as they were two separate regions.
>>
>>
>> Thanks!
>>
>> Shilin
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> 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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Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2016-10-17 Thread Hervé Pagès 

Hi Ramon,

Yes the issue is known. The vsn maintainers have fixed the problem
yesterday in svn, right before the builds started. All the failures
due to vsn not installing on the build machines should be gone in
today's report.

Cheers,
H.

On 10/17/2016 01:34 AM, Ramon Diaz-Uriarte wrote:

Dear All,

Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now
(last 24 to 48 hours?) failing to build in BioC 3.4 in Linux (malbec1) and
Mac OSX (morelia). Looking at the error reports they seem to be due to vsn
not being available. Checking the vsn report
(http://bioconductor.org/checkResults/3.4/bioc-LATEST/vsn) it seems vsn
required R-3.4.0 at the time of the check. However, the new vsn on the svn
repo (v.3.41.8) has

Depends: R (>= 3.0.0), Biobase


So I guess we just need to wait for vsn to be rebuilt? I would normally
just wait quietly, but I am concerned because I think the creation of the
BioC 3.4 release branch is today and release is tomorrow.

Best and apologies for the noise if this issue is known,


R.





--
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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Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2016-10-17 Thread Panagiotis Moulos 
Hi all,

I would like to add also metaseqR in the list of packages failing to 
build in malbec1 and morelia because of vsn. What would be the most 
appropriate course of action for the maintainers? Wait for vsn to be 
correctly built?

Best regards,

Panagiotis


On 10/17/2016 11:34 AM, Ramon Diaz-Uriarte wrote:
> Dear All,
>
> Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now
> (last 24 to 48 hours?) failing to build in BioC 3.4 in Linux (malbec1) and
> Mac OSX (morelia). Looking at the error reports they seem to be due to vsn
> not being available. Checking the vsn report
> (http://bioconductor.org/checkResults/3.4/bioc-LATEST/vsn) it seems vsn
> required R-3.4.0 at the time of the check. However, the new vsn on the svn
> repo (v.3.41.8) has
>
> Depends: R (>= 3.0.0), Biobase
>
>
> So I guess we just need to wait for vsn to be rebuilt? I would normally
> just wait quietly, but I am concerned because I think the creation of the
> BioC 3.4 release branch is today and release is tomorrow.
>
> Best and apologies for the noise if this issue is known,
>
>
> R.
>
>
>

-- 
*Panagiotis Moulos*
Post doctoral researcher
Biomedical Sciences Research Center 'Alexander Fleming'
Fleming 34, 16672, Vari, Greece
e-mail: mou...@fleming.gr 

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[Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2016-10-17 Thread Ramon Diaz-Uriarte 
Dear All,

Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now
(last 24 to 48 hours?) failing to build in BioC 3.4 in Linux (malbec1) and
Mac OSX (morelia). Looking at the error reports they seem to be due to vsn
not being available. Checking the vsn report
(http://bioconductor.org/checkResults/3.4/bioc-LATEST/vsn) it seems vsn
required R-3.4.0 at the time of the check. However, the new vsn on the svn
repo (v.3.41.8) has

Depends: R (>= 3.0.0), Biobase


So I guess we just need to wait for vsn to be rebuilt? I would normally
just wait quietly, but I am concerned because I think the creation of the
BioC 3.4 release branch is today and release is tomorrow.

Best and apologies for the noise if this issue is known,


R.



-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

2016-10-17 Thread Hervé Pagès 

Hi Shilin,

I answered this on the support site:

  https://support.bioconductor.org/p/88232/#88347

Cheers,
H.

On 10/16/2016 08:35 PM, zhao shilin wrote:

Dear BioC team,

I think I found something incorrect in  TxDb.Hsapiens.UCSC.hg38.knownGene,
and reported in https://support.bioconductor.org/p/88232/ but didn't get
reply. I think it is a bug, so decided to send it via email to let you know.

I am using the developing version of TxDb.Hsapiens.UCSC.hg38.knownGene,
because the release version is build in 2015 and has a lot of difference
with UCSC website. Here is the R code for the bug:

require(TxDb.Hsapiens.UCSC.hg38.knownGene)
require(GenomicRanges)

geneDb=TxDb.Hsapiens.UCSC.hg38.knownGene
allGeneRange<-genes(geneDb)
allGeneRange["875"]
txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg38.knownGene)
txs["875"]


We can find CBS gene (txs["875"]) has 25 transcripts, from two
regions: chr21   [6444869, 6467509] and chr21 [43075107, 43076288]

1. CBS gene ("875") was only in chr21 [43075107, 43076288]. The region
of chr21   [6444869, 6467509] was CBSL gene ("102724560"). But CBSL was not
in the database, and its transcripts were recorded in CBS.

2. The gene region of CBS gene (allGeneRange["875"]) was in chr21 [6444869,
43076943], which included all the region between 6444869-43076943. But it
is not correct as they were two separate regions.


Thanks!

Shilin

[[alternative HTML version deleted]]

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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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