Re: [Bioc-devel] Devel nightly build

2017-07-14 Thread Hervé Pagès 

Hi Hector, Val,

The build report for today (Friday Jul 14) is finally here:

  https://bioconductor.org/checkResults/3.6/bioc-LATEST/

I hope you can see the changes you made to your package reflected here
and also that the new version of the package propagated as it should.
Let us know if not.

I introduced a regression when I made some changes a couple of days ago
to the script that generates this report. It's fixed now. Sorry for
that.

As Val said, we've been testing git-based builds as part of the
preparation for the svn->git transition. We're trying as much as
we can to avoid having this testing disrupt the normal functioning
of the daily builds (which are still svn-based!).

Cheers,
H.


On 07/14/2017 01:46 PM, Obenchain, Valerie wrote:

I was wrong about this. Herve has isolated the experimental git-based builds so 
they don't affect the standard svn-based builds at all. I posted about the 
problems we're having with the devel builds here:

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DJuly_011203.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kPBp3A8XCX1agWWYNh78uN9p4Db-hjSVrFfdxXDTtkw=PT_7jq29yh7gjT7hpm8w8vhfkSEVHO0s0xruTkW03kE=

Sorry for the red herring.

Valerie



On 07/14/2017 08:00 AM, Obenchain, Valerie wrote:

Hi Hector,

We are in the beta phase of testing the svn -> git transition so there will be 
a few hicups in the builds over the next week. We hope to have new devel and 
release reports today (July 14).

Thanks for your patience.
Valerie



On 07/14/2017 05:27 AM, Hector Corrada Bravo wrote:

Hello,

I noticed the last SVN snapshot for devel nightly builds was from Monday 7/10. 
Are builds not being done nightly? We want to submit a new package for review 
but need an update to a dependency on the build system we pushed this week.

Thanks for the info!
Hector


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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
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E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Devel nightly build

2017-07-14 Thread Obenchain, Valerie 
I was wrong about this. Herve has isolated the experimental git-based builds so 
they don't affect the standard svn-based builds at all. I posted about the 
problems we're having with the devel builds here:

https://stat.ethz.ch/pipermail/bioc-devel/2017-July/011203.html

Sorry for the red herring.

Valerie



On 07/14/2017 08:00 AM, Obenchain, Valerie wrote:

Hi Hector,

We are in the beta phase of testing the svn -> git transition so there will be 
a few hicups in the builds over the next week. We hope to have new devel and 
release reports today (July 14).

Thanks for your patience.
Valerie



On 07/14/2017 05:27 AM, Hector Corrada Bravo wrote:

Hello,

I noticed the last SVN snapshot for devel nightly builds was from Monday 7/10. 
Are builds not being done nightly? We want to submit a new package for review 
but need an update to a dependency on the build system we pushed this week.

Thanks for the info!
Hector


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Re: [Bioc-devel] push bug fix from devel to release

2017-07-14 Thread Obenchain, Valerie 
Hi,

Instructions are here:

http://www.bioconductor.org/developers/how-to/source-control/

See the section 'Where to commit changes'.

Valerie



On 07/14/2017 07:01 AM, Nathan Olson wrote:

Hi, There is a build error with the release branch of my package
metagenomeFeatures. I fixed the error in the devel branch and would like to
know how to push the changes to the release branch.

Thanks,
Nate Olson

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Re: [Bioc-devel] Devel nightly build

2017-07-14 Thread Obenchain, Valerie 
Hi Hector,

We are in the beta phase of testing the svn -> git transition so there will be 
a few hicups in the builds over the next week. We hope to have new devel and 
release reports today (July 14).

Thanks for your patience.
Valerie



On 07/14/2017 05:27 AM, Hector Corrada Bravo wrote:

Hello,

I noticed the last SVN snapshot for devel nightly builds was from Monday 7/10. 
Are builds not being done nightly? We want to submit a new package for review 
but need an update to a dependency on the build system we pushed this week.

Thanks for the info!
Hector


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[Bioc-devel] push bug fix from devel to release

2017-07-14 Thread Nathan Olson 
Hi, There is a build error with the release branch of my package
metagenomeFeatures. I fixed the error in the devel branch and would like to
know how to push the changes to the release branch.

Thanks,
Nate Olson

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[Bioc-devel] Devel nightly build

2017-07-14 Thread Hector Corrada Bravo 
Hello,

I noticed the last SVN snapshot for devel nightly builds was from Monday 7/10. 
Are builds not being done nightly? We want to submit a new package for review 
but need an update to a dependency on the build system we pushed this week.

Thanks for the info!
Hector


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[Bioc-devel] strand<- method for 'GPos' doesn't work

2017-07-14 Thread Robert Castelo 

hi,

the strand replacement method for 'GPos' objects does not seem to work:

library(GenomicRanges)
example(GPos)
strand(gpos1) <- "-"
Error in methods::slot(object, name) :
  no slot of name "call" for this object of class "GPos"
traceback()
10: methods::slot(object, name)
9: getElement(x, "call")
8: getCall.default(object)
7: getCall(object)
6: update.default(x, strand = value, check = FALSE)
5: update(x, strand = value, check = FALSE)
4: update(x, strand = value, check = FALSE)
3: .local(x, ..., value)
2: `strand<-`(`*tmp*`, value = "-")
1: `strand<-`(`*tmp*`, value = "-")

this kind of operation works perfectly on 'GRanges' objects, so i guess 
it should also work also with 'GPos' objects:


example(GRanges)
gr1
GRanges object with 1 range and 0 metadata columns:
  seqnamesranges strand

  [1] chr2 [56, 125]  *
  ---
  seqinfo: 1 sequence from an unspecified genome; no seqlength
strand(gr1) <- "-"
gr1
GRanges object with 1 range and 0 metadata columns:
  seqnamesranges strand

  [1] chr2 [56, 125]  -
  ---
  seqinfo: 1 sequence from an unspecified genome; no seqlengths


below my session info. thanks!

robert.
ps: sessionInfo()
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
 [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
 [7] LC_PAPER=en_US.UTF8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2  IRanges_2.10.2
[4] S4Vectors_0.14.3 BiocGenerics_0.22.0  colorout_1.1-2

loaded via a namespace (and not attached):
[1] zlibbioc_1.22.0 compiler_3.4.0  tools_3.4.0
[4] XVector_0.16.0  GenomeInfoDbData_0.99.0 RCurl_1.95-4.8
[7] bitops_1.0-6

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