Re: [Bioc-devel] daily build failures for the trena package, related to BSgenome.Hsapiens.UCSC.hg38 2bit file

2019-05-22 Thread Martin Morgan 
I tried to reproduce the commands reported by the build system. So on a fresh 
git clone

  $ cd /tmp
  $ git clone g...@git.bioconductor.org:packages/trena
  $ R -vanilla CMD build --keep-empty-dirs --no-resave-data trena

(the buld system doesn't use vanilla, but I have an ~/.Rprofile and maybe other 
things, and I'm doing my best not to introduce extraneous stuff). I then tried 
to check as the build system does

R --vanilla CMD check --install=check:trena.install-out.txt 
--library=/Users/ma38727/bin/R-3-6-branch/library --no-vignettes --timings 
trena_1.7.1.tar.gz

where I tried various arguments for --library (an empty directory; the 
directory shown here which is the location my R is installed; the directory 
where my non-base R packages are installed, the current directory, the 
directory containing trena source, :-separated directories). I'd end up either 
with

* checking whether package ‘trena’ can be installed ... ERROR
Installation failed.
See ‘/private/tmp/trena.Rcheck/00install.out’ for details.
* DONE

or (if 'trena.install-out.txt' didn't exist in the cwd)

* checking whether package ‘trena’ can be installed ... ERROR
install log ‘’ does not exist
* DONE

I couldn't find helpful documentation (other than R CMD check --help) on what 
value --library= should take; maybe Hervé or other build system wiz can provide 
guidance so that we can exactly reproduce what the build system is doing?

I doubt any of the following is the magic bullet, but...

When I built and checked this on my local machine I received a warning and then 
error

* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
...
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:

  1 Test Suite :
  trena RUnit Tests - 87 test functions, 1 error, 0 failures
  ERROR in test_findMatchesByChromosomalRegion.yeast: Error in 
loadNamespace(name) :
there is no package called 'BSgenome.Scerevisiae.UCSC.sacCer3'

because 'BSgenome.Scerevisiae.UCSC.sacCer3' is not listed in the Suggests: 
field of your package; are there other missing dependencies?

In the build report, it's weird to see 

[1] --- test_createGeneModelFromRegulatoryRegions
Called from: test_createGeneModelFromRegulatoryRegions()
Browse[1]> debug: checkTrue(nrow(tbl.geneModel) > 40)

which suggests that there is a stray browser() call in your code

$ grep -r browser *
...
inst/misc/multiModels/aqp4.R:  browser()
inst/misc/multiModels/aqp4.R:   browser()
inst/misc/multiModels/aqp4.R:   browser()
inst/misc/multiModels/aqp4-multi.R:  browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser();
inst/unitTests/test_Trena.R:browser()
inst/utils/evaluateAllSolvers.R:browser()
inst/utils/TReNA.R:browser()

In trena.Rcheck/tests/runTests.Rout

I see 

[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = 
targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay 
matrix
...
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = 
targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay 
matrix

i.e., the same test running twice. Why is that?

I notice that there are .DS_store files in your repository that shouldn't be 
there

trena master$ find . -name ".*"
.
./man/.DS_Store
./.Rbuildignore
./.gitignore
./.git
./inst/misc/.DS_Store
./inst/.DS_Store
./inst/demos/.DS_Store

Maybe resolving some of these issues, especially the last, helps to resolve 
problems?

Martin

On 5/22/19, 2:34 PM, "Bioc-devel on behalf of Paul Shannon" 
 
wrote:

I get daily R CMD check failures visible at

  
https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html

The recurring failure, which I cannot replicate on my own systems, is due 
to this error:

test_.getScoredMotifs Warning in .seqlengths_TwoBitFile(x) : mustOpen: 

Can't open 
/home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit
 to read: No such file or directory


If this is my error, I’d be glad to fix it - though I will need some 
guidance on how to do so.

Thank you,

 - Paul
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[Bioc-devel] daily build failures for the trena package, related to BSgenome.Hsapiens.UCSC.hg38 2bit file

2019-05-22 Thread Paul Shannon 
I get daily R CMD check failures visible at

  
https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html

The recurring failure, which I cannot replicate on my own systems, is due to 
this error:

test_.getScoredMotifs Warning in .seqlengths_TwoBitFile(x) : mustOpen: 

Can't open 
/home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit
 to read: No such file or directory


If this is my error, I’d be glad to fix it - though I will need some guidance 
on how to do so.

Thank you,

 - Paul
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Re: [Bioc-devel] Daily build

2018-03-12 Thread Shepherd, Lori 
It looks like this was just a latency issue for updating.  After the build 
completes it can take some additional time for the files to be redirected.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Obenchain, 
Valerie 
Sent: Friday, March 9, 2018 11:35:38 AM
To: Nicolas Descostes; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Daily build

That sounds like a bug. Thanks for the report, we'll look into it.

Valerie


On 03/09/2018 07:48 AM, Nicolas Descostes wrote:
I mean that on the landing page: 
https://bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html

If you click on NEWS 
(https://bioconductor.org/packages/3.7/bioc/news/ChIPSeqSpike/NEWS), the file 
is not up to date. However, if you download ChIPSeqSpike_0.99.21.tar.gz and 
open the file NEWS, it is indeed the last one. So the modification is not 
reported on the landing page.

2018-03-09 10:40 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
What do you mean by 'the NEWS file has not been properly updated'? Did you 
commit a change before the builds started, bumped the package version and the 
package you downloaded with biocLite() was somehow out of date? Or was a 
download from the landing page out of date ... ?

Valerie




On 03/09/2018 07:25 AM, Nicolas Descostes wrote:
Dear Valerie,

My package has been correctly updated except for the file NEWS. 
https://bioconductor.org/packages/3.7/bioc/news/ChIPSeqSpike/NEWS

Is it an issue that I should report on the bioc-devel. Have you been aware of 
this problem with other users?

Thanks.

Nicolas

2018-03-07 17:02 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Do a pull and check the log. Your commit should appear in the log.

The builds run once a day and start at 5pm EST. The report posts the following 
day (see time at top of report). If your commit was before 5pm it will be 
included in the build tonight. Otherwise the changes will be picked up tomorrow 
(posted Friday).

Valerie




On 03/07/2018 01:56 PM, Nicolas Descostes wrote:
Hi Valerie,

I corrected a few things and followed the instructions from the beginning 
(using the eclipse interface). I pushed successfully. I would like to know if 
the commit date should appear right away at 
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C or if there can be a 
delay?

I double checked with the command:

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git push
Everything up-to-date

Thank you,

Nicolas

2018-03-07 12:47 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Hi Nicolas,

This is the last commit I see in the master branch for ChIPSeqSpike:

commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, 
origin/HEAD)
Author: kitano902 
<mailto:nicolas.descos...@nyumc.org>
Date:   Fri Jan 26 14:29:26 2018 -0500

remove '{' in count.Rd

The most recent commits are not making it to 
g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>. At one point you 
had the workflow down and were able to make commits. You may want to revisit 
the documentation for troubleshooting tips:

https://www.bioconductor.org/developers/how-to/git/

Valerie




On 03/07/2018 05:12 AM, Nicolas Descostes wrote:

Dear community,

When my package ChIPSeqSpike was accepted, I have been noticed that no
further action was required regarding my github (
https://github.com/descostesn/ChIPSeqSpike).

I did two commits with version bump yesterday and I did not receive any
notification. I checked the version at
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C
 and the commits
of yesterday do not appear. I am using egit with eclipse oxygen. I went
through the bioc doc but I think that I followed everything.

Did I miss something?

Thanks.

Nicolas

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Re: [Bioc-devel] Daily build

2018-03-09 Thread Obenchain, Valerie 
That sounds like a bug. Thanks for the report, we'll look into it.

Valerie


On 03/09/2018 07:48 AM, Nicolas Descostes wrote:
I mean that on the landing page: 
https://bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html

If you click on NEWS 
(https://bioconductor.org/packages/3.7/bioc/news/ChIPSeqSpike/NEWS), the file 
is not up to date. However, if you download ChIPSeqSpike_0.99.21.tar.gz and 
open the file NEWS, it is indeed the last one. So the modification is not 
reported on the landing page.

2018-03-09 10:40 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
What do you mean by 'the NEWS file has not been properly updated'? Did you 
commit a change before the builds started, bumped the package version and the 
package you downloaded with biocLite() was somehow out of date? Or was a 
download from the landing page out of date ... ?

Valerie




On 03/09/2018 07:25 AM, Nicolas Descostes wrote:
Dear Valerie,

My package has been correctly updated except for the file NEWS. 
https://bioconductor.org/packages/3.7/bioc/news/ChIPSeqSpike/NEWS

Is it an issue that I should report on the bioc-devel. Have you been aware of 
this problem with other users?

Thanks.

Nicolas

2018-03-07 17:02 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Do a pull and check the log. Your commit should appear in the log.

The builds run once a day and start at 5pm EST. The report posts the following 
day (see time at top of report). If your commit was before 5pm it will be 
included in the build tonight. Otherwise the changes will be picked up tomorrow 
(posted Friday).

Valerie




On 03/07/2018 01:56 PM, Nicolas Descostes wrote:
Hi Valerie,

I corrected a few things and followed the instructions from the beginning 
(using the eclipse interface). I pushed successfully. I would like to know if 
the commit date should appear right away at 
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C or if there can be a 
delay?

I double checked with the command:

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git push
Everything up-to-date

Thank you,

Nicolas

2018-03-07 12:47 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Hi Nicolas,

This is the last commit I see in the master branch for ChIPSeqSpike:

commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, 
origin/HEAD)
Author: kitano902 

Date:   Fri Jan 26 14:29:26 2018 -0500

remove '{' in count.Rd

The most recent commits are not making it to 
g...@git.bioconductor.org. At one point you 
had the workflow down and were able to make commits. You may want to revisit 
the documentation for troubleshooting tips:

https://www.bioconductor.org/developers/how-to/git/

Valerie




On 03/07/2018 05:12 AM, Nicolas Descostes wrote:

Dear community,

When my package ChIPSeqSpike was accepted, I have been noticed that no
further action was required regarding my github (
https://github.com/descostesn/ChIPSeqSpike).

I did two commits with version bump yesterday and I did not receive any
notification. I checked the version at
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C
 and the commits
of yesterday do not appear. I am using egit with eclipse oxygen. I went
through the bioc doc but I think that I followed everything.

Did I miss something?

Thanks.

Nicolas

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Daily build

2018-03-09 Thread Obenchain, Valerie 
What do you mean by 'the NEWS file has not been properly updated'? Did you 
commit a change before the builds started, bumped the package version and the 
package you downloaded with biocLite() was somehow out of date? Or was a 
download from the landing page out of date ... ?

Valerie



On 03/09/2018 07:25 AM, Nicolas Descostes wrote:
Dear Valerie,

My package has been correctly updated except for the file NEWS. 
https://bioconductor.org/packages/3.7/bioc/news/ChIPSeqSpike/NEWS

Is it an issue that I should report on the bioc-devel. Have you been aware of 
this problem with other users?

Thanks.

Nicolas

2018-03-07 17:02 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Do a pull and check the log. Your commit should appear in the log.

The builds run once a day and start at 5pm EST. The report posts the following 
day (see time at top of report). If your commit was before 5pm it will be 
included in the build tonight. Otherwise the changes will be picked up tomorrow 
(posted Friday).

Valerie




On 03/07/2018 01:56 PM, Nicolas Descostes wrote:
Hi Valerie,

I corrected a few things and followed the instructions from the beginning 
(using the eclipse interface). I pushed successfully. I would like to know if 
the commit date should appear right away at 
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C or if there can be a 
delay?

I double checked with the command:

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git push
Everything up-to-date

Thank you,

Nicolas

2018-03-07 12:47 GMT-05:00 Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>>:
Hi Nicolas,

This is the last commit I see in the master branch for ChIPSeqSpike:

commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, 
origin/HEAD)
Author: kitano902 

Date:   Fri Jan 26 14:29:26 2018 -0500

remove '{' in count.Rd

The most recent commits are not making it to 
g...@git.bioconductor.org. At one point you 
had the workflow down and were able to make commits. You may want to revisit 
the documentation for troubleshooting tips:

https://www.bioconductor.org/developers/how-to/git/

Valerie




On 03/07/2018 05:12 AM, Nicolas Descostes wrote:

Dear community,

When my package ChIPSeqSpike was accepted, I have been noticed that no
further action was required regarding my github (
https://github.com/descostesn/ChIPSeqSpike).

I did two commits with version bump yesterday and I did not receive any
notification. I checked the version at
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C
 and the commits
of yesterday do not appear. I am using egit with eclipse oxygen. I went
through the bioc doc but I think that I followed everything.

Did I miss something?

Thanks.

Nicolas

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Daily build

2018-03-07 Thread Obenchain, Valerie 
Hi Nicolas,

This is the last commit I see in the master branch for ChIPSeqSpike:

commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, 
origin/HEAD)
Author: kitano902 

Date:   Fri Jan 26 14:29:26 2018 -0500

remove '{' in count.Rd

The most recent commits are not making it to 
g...@git.bioconductor.org. At one point you 
had the workflow down and were able to make commits. You may want to revisit 
the documentation for troubleshooting tips:

https://www.bioconductor.org/developers/how-to/git/

Valerie



On 03/07/2018 05:12 AM, Nicolas Descostes wrote:

Dear community,

When my package ChIPSeqSpike was accepted, I have been noticed that no
further action was required regarding my github (
https://github.com/descostesn/ChIPSeqSpike).

I did two commits with version bump yesterday and I did not receive any
notification. I checked the version at
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C and the commits
of yesterday do not appear. I am using egit with eclipse oxygen. I went
through the bioc doc but I think that I followed everything.

Did I miss something?

Thanks.

Nicolas

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[Bioc-devel] Daily build

2018-03-07 Thread Nicolas Descostes 
Dear community,

When my package ChIPSeqSpike was accepted, I have been noticed that no
further action was required regarding my github (
https://github.com/descostesn/ChIPSeqSpike).

I did two commits with version bump yesterday and I did not receive any
notification. I checked the version at
https://bioconductor.org/checkResults/devel/bioc-LATEST/#C and the commits
of yesterday do not appear. I am using egit with eclipse oxygen. I went
through the bioc doc but I think that I followed everything.

Did I miss something?

Thanks.

Nicolas

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Re: [Bioc-devel] daily build system behind

2014-09-09 Thread Andrzej Oleś 
Dear Levi,

please note that experiment data packages are now build just twice a week, on
Wednesdays and Saturdays. So no need to worry.

Cheers,
Andrzej

On Tue, Sep 9, 2014 at 5:01 PM, Levi Waldron
 wrote:
> I just noticed that the daily build systems are several days behind, eg for
> experimental data packages:
>
> http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/
>
> Snapshot Date: 2014-09-06 06:15:22 -0700 (Sat, 06 Sep 2014)
> URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
> Last Changed Rev: 2991 / Revision: 2991
> Last Changed Date: 2014-09-02 08:08:09 -0700 (Tue, 02 Sep 2014)
>
>
> --
> Levi Waldron
> Assistant Professor of Biostatistics
> City University of New York School of Public Health, Hunter College
> 2180 3rd Ave Rm 538
> New York NY 10035-4003
> phone: 212-396-7747
> www.waldronlab.org
>
> [[alternative HTML version deleted]]
>
> ___
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[Bioc-devel] daily build system behind

2014-09-09 Thread Levi Waldron 
I just noticed that the daily build systems are several days behind, eg for
experimental data packages:

http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/

Snapshot Date: 2014-09-06 06:15:22 -0700 (Sat, 06 Sep 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
Last Changed Rev: 2991 / Revision: 2991
Last Changed Date: 2014-09-02 08:08:09 -0700 (Tue, 02 Sep 2014)


-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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Re: [Bioc-devel] daily build problems, how to debug?

2014-02-13 Thread Dan Tenenbaum 


- Original Message -
> From: "Dan Tenenbaum" 
> To: "J. Hettling" 
> Cc: bioc-devel@r-project.org
> Sent: Thursday, February 13, 2014 8:08:16 AM
> Subject: Re: [Bioc-devel] daily build problems, how to debug?
> 
> 
> 
> - Original Message -
> > From: "J. Hettling" 
> > To: bioc-devel@r-project.org
> > Sent: Thursday, February 13, 2014 4:29:21 AM
> > Subject: [Bioc-devel] daily build problems, how to debug?
> > 
> > Dear Bioconductor developers,
> > 
> > since updating our package 'BiGGR' on the development branch, the
> > daily built gives errors
> > (see
> > http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/BiGGR/zin2-buildsrc.html).
> > 
> > However, on both of my machines R CMD build and R CMD check run
> > without problems (one of them actually running the same OS version
> > as zin2).
> > I see that there are some Latex errors in the vignette building,
> > but
> > cannot really make sense of it.
> > 
> > My current approach is trial-and-error, I change what I suspect
> > would
> > cause the error, update the devel package and wait a day until it
> > is
> > build again.
> > 
> > Is there a better way to debug this?
> > 
> 
> Looks like you had an unnecessary Makefile in vignettes/. It wasn't
> doing anything that R does not automatically do. I removed it and
> the package now builds successfully, so I went ahead and committed
> that change.
> 

This will not be reflected on the build system until tomorrow morning (Seattle 
time).

Dan

> Dan
> 
> 
> 
> > Kind Regards
> > 
> > Hannes
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
>

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Re: [Bioc-devel] daily build problems, how to debug?

2014-02-13 Thread Dan Tenenbaum 


- Original Message -
> From: "J. Hettling" 
> To: bioc-devel@r-project.org
> Sent: Thursday, February 13, 2014 4:29:21 AM
> Subject: [Bioc-devel] daily build problems, how to debug?
> 
> Dear Bioconductor developers,
> 
> since updating our package 'BiGGR' on the development branch, the
> daily built gives errors
> (see
> http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/BiGGR/zin2-buildsrc.html).
> 
> However, on both of my machines R CMD build and R CMD check run
> without problems (one of them actually running the same OS version
> as zin2).
> I see that there are some Latex errors in the vignette building, but
> cannot really make sense of it.
> 
> My current approach is trial-and-error, I change what I suspect would
> cause the error, update the devel package and wait a day until it is
> build again.
> 
> Is there a better way to debug this?
> 

Looks like you had an unnecessary Makefile in vignettes/. It wasn't doing 
anything that R does not automatically do. I removed it and the package now 
builds successfully, so I went ahead and committed that change.

Dan



> Kind Regards
> 
> Hannes
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] daily build problems, how to debug?

2014-02-13 Thread Kasper Daniel Hansen 
Hannes,

I think (but don't know) that there is something happening with the build
servers these days.  The Windows machine has disappeared.  This sometimes
happens and I would just wait a day or two.  Perhaps the build team can
comment?

Best,
Kasper


On Thu, Feb 13, 2014 at 8:58 AM, Cristobal Fresno Rodríguez <
cristobalfre...@gmail.com> wrote:

> Hi Hannes,
>
> Are you using the "*R devel engine*" installed in zin2 (R Under development
> (unstable) (2014-01-15 r64790) -- "Unsuffered Consequences")? and then
> installed "*devel BiocLite 2.14*"?
>
> Regards,
>
> Cristobal
>
>
> 2014-02-13 9:29 GMT-03:00 Hettling, J. :
>
> > Dear Bioconductor developers,
> >
> > since updating our package 'BiGGR' on the development branch, the daily
> > built gives errors
> > (see
> >
> http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/BiGGR/zin2-buildsrc.html
> > ).
> >
> > However, on both of my machines R CMD build and R CMD check run without
> > problems (one of them actually running the same OS version as zin2).
> > I see that there are some Latex errors in the vignette building, but
> > cannot really make sense of it.
> >
> > My current approach is trial-and-error, I change what I suspect would
> > cause the error, update the devel package and wait a day until it is
> build
> > again.
> >
> > Is there a better way to debug this?
> >
> > Kind Regards
> >
> > Hannes
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] daily build problems, how to debug?

2014-02-13 Thread Cristobal Fresno Rodríguez 
Hi Hannes,

Are you using the "*R devel engine*" installed in zin2 (R Under development
(unstable) (2014-01-15 r64790) -- "Unsuffered Consequences")? and then
installed "*devel BiocLite 2.14*"?

Regards,

Cristobal


2014-02-13 9:29 GMT-03:00 Hettling, J. :

> Dear Bioconductor developers,
>
> since updating our package 'BiGGR' on the development branch, the daily
> built gives errors
> (see
> http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/BiGGR/zin2-buildsrc.html
> ).
>
> However, on both of my machines R CMD build and R CMD check run without
> problems (one of them actually running the same OS version as zin2).
> I see that there are some Latex errors in the vignette building, but
> cannot really make sense of it.
>
> My current approach is trial-and-error, I change what I suspect would
> cause the error, update the devel package and wait a day until it is build
> again.
>
> Is there a better way to debug this?
>
> Kind Regards
>
> Hannes
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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[Bioc-devel] daily build problems, how to debug?

2014-02-13 Thread Hettling, J. 
Dear Bioconductor developers,

since updating our package 'BiGGR' on the development branch, the daily built 
gives errors
(see 
http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/BiGGR/zin2-buildsrc.html).

However, on both of my machines R CMD build and R CMD check run without 
problems (one of them actually running the same OS version as zin2).
I see that there are some Latex errors in the vignette building, but cannot 
really make sense of it.

My current approach is trial-and-error, I change what I suspect would cause the 
error, update the devel package and wait a day until it is build again.

Is there a better way to debug this?

Kind Regards

Hannes

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