[Bioc-devel] GateFinder Write Permission

[Tony Culos]

Hey Nima,

I have been told I do not actually have write access to GateFinder and need
to get your permission to access the package.

Thanks,
Tony

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Re: [Bioc-devel] Bioconductor Git Access: GateFinder

[Turaga, Nitesh]

Hi Tony,

Another thing, I checked your Github repo. Please do not push a commit like 
this to upstream, "test commit: changing name and pushing to test upstream 
access”.

The Bioconductor version of the repo is canonical. You cannot go back in time 
on that repo. You can test upstream access by using `ssh -T 
g...@git.bioconductor.org`.

Best,

Nitesh


> On Apr 13, 2018, at 2:43 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Tony,
> 
> You don’t have access to that package. I’ve checked the package DESCRIPTION 
> and there is no record of you. Please ask the authors for access to the 
> package. 
> 
> Author: Nima Aghaeepour , Erin F. Simonds 
> 
> Maintainer: Nima Aghaeepour 
> 
> Copy bioc-devel on the email where you ask the authors for permission. It is 
> always easier to contribute to their Github repo. 
> 
> Best,
> 
> Nitesh 
> 
>> On Apr 13, 2018, at 2:30 PM, Tony Culos  wrote:
>> 
>> I've changed it to SSH but still do not have write access to GateFinder 
>> 
>> git remote -v
>> origin   g...@github.com:Teculos/GateFinder.git (fetch)
>> origin   g...@github.com:Teculos/GateFinder.git (push)
>> upstream g...@git.bioconductor.org:packages/GateFinder.git (fetch)
>> upstream g...@git.bioconductor.org:packages/GateFinder.git (push)
>> 
>> ssh -T g...@git.bioconductor.org command lists all packages as read only
>> 
>> On Fri, Apr 13, 2018 at 10:59 AM, Turaga, Nitesh 
>>  wrote:
>> You are using the HTTPS protocol instead of SSH. Please refer to 
>> http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream 
>> should look like “g...@git.bioconductor.org:packages/GateFinder.git”.
>> 
>> 
>> Nitesh 
>> 
>> 
>> 
>>> On Apr 13, 2018, at 1:44 PM, Tony Culos  wrote:
>>> 
>>> Hello,
>>> 
>>> I recently received an email from maintai...@bioconductor.org saying that I
>>> have access to the GateFinder package however when I try the command "git
>>> push upstream master", I receive the error:
>>> 
>>> fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by
>>> fallthru
>>> (or you mis-spelled the reponame)
>>> 
>>> Also the results for "git remote -v" are:
>>> 
>>> origin https://github.com/Teculos/GateFinder.git (fetch)
>>> origin https://github.com/Teculos/GateFinder.git (push)
>>> upstream https://git.bioconductor.org/packages/GateFinder (fetch)
>>> upstream https://git.bioconductor.org/packages/GateFinder (push)
>>> 
>>> Thank You,
>>> Tony C.
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> ___
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>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
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> 



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[Bioc-devel] Fwd: Bioconductor Git Access: GateFinder

[Turaga, Nitesh]

Begin forwarded message:

From: ni41435_ca 
>
Subject: Re: [Bioc-devel] Bioconductor Git Access: GateFinder
Date: April 13, 2018 at 2:43:04 PM EDT
To: Tony Culos >
Cc: bioc-devel >

Hi Tony,

You don’t have access to that package. I’ve checked the package DESCRIPTION and 
there is no record of you. Please ask the authors for access to the package.

Author: Nima Aghaeepour >, Erin 
F. Simonds >
Maintainer: Nima Aghaeepour >

Copy bioc-devel on the email where you ask the authors for permission. It is 
always easier to contribute to their Github repo.

Best,

Nitesh

On Apr 13, 2018, at 2:30 PM, Tony Culos 
> wrote:

I've changed it to SSH but still do not have write access to GateFinder

git remote -v
origin g...@github.com:Teculos/GateFinder.git (fetch)
origin g...@github.com:Teculos/GateFinder.git (push)
upstream 
g...@git.bioconductor.org:packages/GateFinder.git
 (fetch)
upstream 
g...@git.bioconductor.org:packages/GateFinder.git
 (push)

ssh -T g...@git.bioconductor.org command 
lists all packages as read only

On Fri, Apr 13, 2018 at 10:59 AM, Turaga, Nitesh 
> wrote:
You are using the HTTPS protocol instead of SSH. Please refer to 
http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream should 
look like 
“g...@git.bioconductor.org:packages/GateFinder.git”.


Nitesh



On Apr 13, 2018, at 1:44 PM, Tony Culos 
> wrote:

Hello,

I recently received an email from 
maintai...@bioconductor.org saying that I
have access to the GateFinder package however when I try the command "git
push upstream master", I receive the error:

fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by
fallthru
(or you mis-spelled the reponame)

Also the results for "git remote -v" are:

origin https://github.com/Teculos/GateFinder.git (fetch)
origin https://github.com/Teculos/GateFinder.git (push)
upstream https://git.bioconductor.org/packages/GateFinder (fetch)
upstream https://git.bioconductor.org/packages/GateFinder (push)

Thank You,
Tony C.

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Re: [Bioc-devel] Bioconductor Git Access: GateFinder

[Turaga, Nitesh]

Hi Tony,

You don’t have access to that package. I’ve checked the package DESCRIPTION and 
there is no record of you. Please ask the authors for access to the package. 

Author: Nima Aghaeepour , Erin F. Simonds 

Maintainer: Nima Aghaeepour 

Copy bioc-devel on the email where you ask the authors for permission. It is 
always easier to contribute to their Github repo. 

Best,

Nitesh 

> On Apr 13, 2018, at 2:30 PM, Tony Culos  wrote:
> 
> I've changed it to SSH but still do not have write access to GateFinder 
> 
> git remote -v
> origing...@github.com:Teculos/GateFinder.git (fetch)
> origing...@github.com:Teculos/GateFinder.git (push)
> upstream  g...@git.bioconductor.org:packages/GateFinder.git (fetch)
> upstream  g...@git.bioconductor.org:packages/GateFinder.git (push)
> 
> ssh -T g...@git.bioconductor.org command lists all packages as read only
> 
> On Fri, Apr 13, 2018 at 10:59 AM, Turaga, Nitesh 
>  wrote:
> You are using the HTTPS protocol instead of SSH. Please refer to 
> http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream 
> should look like “g...@git.bioconductor.org:packages/GateFinder.git”.
> 
> 
> Nitesh 
> 
> 
> 
> > On Apr 13, 2018, at 1:44 PM, Tony Culos  wrote:
> > 
> > Hello,
> > 
> > I recently received an email from maintai...@bioconductor.org saying that I
> > have access to the GateFinder package however when I try the command "git
> > push upstream master", I receive the error:
> > 
> > fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by
> > fallthru
> > (or you mis-spelled the reponame)
> > 
> > Also the results for "git remote -v" are:
> > 
> > origin https://github.com/Teculos/GateFinder.git (fetch)
> > origin https://github.com/Teculos/GateFinder.git (push)
> > upstream https://git.bioconductor.org/packages/GateFinder (fetch)
> > upstream https://git.bioconductor.org/packages/GateFinder (push)
> > 
> > Thank You,
> > Tony C.
> > 
> >   [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
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> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> 



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Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Thank you Andrzej for the info!


## Re-point (1)

Regarding my (1), I got my github repo in sync following
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and 
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
It all worked without problems. Thanks again for the great docs!


## on.bioc auto-detection

At 
https://github.com/LieberInstitute/recountWorkflow/commit/b456fbbe6ddbeda297ef03b79de9e004f28c0b97#diff-a87d0071c97357f224ad6608f837fbbfR45
I'm using

on.bioc <- knitr::opts_knit$get("rmarkdown.pandoc.to") != 'latex'

to detect automatically whether I'm rendering the output for Bioc or
not. For F1000 I'll use BiocWorkflowTools::f1000_article as the output
by calling rmarkdown::render() manually. I thought this little code
would help others who want to have a single repo for both BioC and
F1000.


## Re-point (5)

>From Lori's email that she sent today, I can see at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/recountWorkflow/malbec2-buildwebvig.html
how the final Bioc web version is being built. That is:

/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
output_format="BiocStyle:::html_fragment")' &&
/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
".buildwebvig/recountWorkflow/recount-workflow.R")'

I can see the R version being used at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/index.html
although not the bioc version (that I can infer from the package
loading messages, like clusterProfiler's one). This only matters in
those 6 months when release/devel are being built on the same R
version.

Now that I have the commands and versions, if I ever see anything
weird on the rendered Bioc web version I have a way to test things
myself instead of relying on the bioc builds. Since this is a bit
different than the rest of Bioc, maybe it'd be good to document the
build commands somewhere else.



Again, let me thank all of you for your work! I'm really excited about
the new workflow build chain and how it'll simplify
maintaining/writing workflows!


Best,
Leo

On Tue, Apr 3, 2018 at 6:38 AM, Andrzej Oleś  wrote:
>
> Dear Leo,
>
> thanks for you inquiry. Re points 2-4: there is no need to use the token file 
> .html_output anymore. This was an intermediate solution meant for the 
> transition period to new output format. Now all workflow vignettes for the 
> the website are build using this new format, regardless the `output` setting 
> in the vignette YAML header. Note that the format set in the vignette is 
> still used to render the document distributed with the package tarball.
>
> Cheers,
> Andrzej
>
>
> On Mon, Apr 2, 2018 at 4:32 PM, Leonardo Collado Torres  
> wrote:
>>
>> Hi,
>>
>> Thank you for all the work in this transition Andrzej, Lori, Valerie,
>> Nitesh and Hervé!
>>
>>
>> I have a few questions about the new system.
>>
>> 1) I already had a github repo (that I manually kept in sync with the
>> subversion one) for the recountWorkflow. Should I just follow the
>> instructions at
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
>> I guess that I'll need to do this too
>> http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>
>> 2) Is repo/vignettes/.html_output still needed?
>>
>> 3) Related to (2), the .html_output file used to ignore the `output`
>> line in the vignette YAML. I got an email from Lori saying that
>> output: BiocWorkflowTools::f1000_article is not working for
>> recountWorfkflow for now (no html vignette). My guess is that the
>> `output` line now matters, and in my case, that would build a pdf file
>> which is ignored due to
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
>> in my .Rbuildignore.
>>
>> 4) Related to the last 2. What setup do you recommend so I can
>> maintain a single git repo that produces the files needed for
>> uploading them to F1000research? Before this transition, I had to
>> maintain 3 repos: the subversion one for Bioc, my git copy (well,
>> main), and another one with the files setup for F1000. At some point
>> in the past, Andrzej recommended that I use "output:
>> BiocWorkflowTools::f1000_article" to try to have all the files in 1
>> place. I imagine that I would still need some ifelse() statements for
>> sentences like the one I have at
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
>> I think that this question could be generalized and documented in the
>> Bioc website.
>>
>> 5) Is there anything else I should be aware of so I can reproduce any
>> errors? In the past, the Bioc workflow system would trigger a build
>> immediately after a new push, and due to the custom way workflows were
>> built (like .html_output), I 

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

[Turaga, Nitesh]

You are using the HTTPS protocol instead of SSH. Please refer to 
http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream should 
look like “g...@git.bioconductor.org:packages/GateFinder.git”.


Nitesh 



> On Apr 13, 2018, at 1:44 PM, Tony Culos  wrote:
> 
> Hello,
> 
> I recently received an email from maintai...@bioconductor.org saying that I
> have access to the GateFinder package however when I try the command "git
> push upstream master", I receive the error:
> 
> fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by
> fallthru
> (or you mis-spelled the reponame)
> 
> Also the results for "git remote -v" are:
> 
> origin https://github.com/Teculos/GateFinder.git (fetch)
> origin https://github.com/Teculos/GateFinder.git (push)
> upstream https://git.bioconductor.org/packages/GateFinder (fetch)
> upstream https://git.bioconductor.org/packages/GateFinder (push)
> 
> Thank You,
> Tony C.
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] TIMEOUT on package MEAL

[Shepherd, Lori]

It is by fluke that the windows did not time out... The builders timeout occur 
at 2400 sec and you are right up against the edge at 2145.4 seconds on windows.


The build reports include an EllapsedTime  indication in the summary section 
for each builder ...


Your package does not meet the requirement (<2400 (40min!!)  and your vignette 
needs to be altered to fit the time constraints of the builders.


You should easily be able to test R CMD build on your system and log the time 
to debug this issue. On linux there is the `time `  option.




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 Carlos Ruiz 

Sent: Friday, April 13, 2018 11:26:03 AM
To: Turaga, Nitesh; Bioc-devel
Subject: Re: [Bioc-devel] TIMEOUT on package MEAL

Hi BiocDevel,

Could you help me with this issue? The report is not very informative. I
suspect that the vignettes are taking too long but I have two vignettes
and I don't know which one is more problematic. I don't understand
either why I have a timeout in OS and Linux but not in Windows.

When I had to deal with warnings or errors, I was able to reproduce them
in my computer and solve them. Is there any way to reproduce the timeouts?

Thank you,

Carlos Ruiz


El 12/04/2018 a las 18:22, Turaga, Nitesh escribi�:
> Dear maintainer,
>
> I'd like to bring to your attention that the  your package is getting a 
> TIMEOUT 'R CMD build' on platforms in the devel version of Bioconductor (i.e. 
> BioC 3.7):
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.html
>
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if you have any question or need help.
>
> The package is failing on devel which is very problematic. If it is not fixed 
> in devel in a timely manner we would also consider this package for potential 
> deprecation in the next cycle.  The deadline for passing R CMD build and 
> check in devel is April 25.
>
> Thanks for your contribution to Bioconductor.
>
> Pleae be advised that Bioconductor has switched from svn to Git. Some helpful
> links can be found here:
> https://bioconductor.org/developers/how-to/git/
>
> Best,
>
> Nitesh Turaga
> Bioconductor Core Team
>
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--
Carlos Ruiz
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08003 Barcelona, Spain
Tel. +34 93 214 7309
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[Bioc-devel] Bioconductor Git Access: GateFinder

[Tony Culos]

Hello,

I recently received an email from maintai...@bioconductor.org saying that I
have access to the GateFinder package however when I try the command "git
push upstream master", I receive the error:

fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by
fallthru
(or you mis-spelled the reponame)

Also the results for "git remote -v" are:

origin https://github.com/Teculos/GateFinder.git (fetch)
origin https://github.com/Teculos/GateFinder.git (push)
upstream https://git.bioconductor.org/packages/GateFinder (fetch)
upstream https://git.bioconductor.org/packages/GateFinder (push)

Thank You,
Tony C.

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Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

[Davide Risso]

Hi Michael,

Thanks for looking into this.

Can you or someone with push permission to S4Vectors implement the workaround 
that you mentioned?

Happy to create a pull request on Github if that helps.

We’re trying to solve this to fix the clusterExperiment package build on 
Bioc-devel.

Thanks,
Davide


On Apr 12, 2018, at 1:27 PM, Michael Lawrence 
> wrote:

Yea it's basically

library(S4Vectors)
library(RNeXML)
is(1:5, "Annotated")
# Found more than one class "Annotated" in cache; using the first,
from namespace 'S4Vectors'
# Also defined by ‘RNeXML’
# [1] FALSE

But can be worked around:
is(1:5, getClass("Annotated", where=getNamespace("S4Vectors"))
# [1] FALSE

Of course, using class objects instead of class names in every call to
is() is not very palatable, but that's how it's done in all other
languages, as far as I know.

There is an inconsistency between new() and is() when resolving the
class name. new() looks into the calling package's namespace, while
is() looks at the package for the class of the 'object'. The new()
approach seems sensible for that function, since packages should be
abstracting the construction of their objects with constructors. The
is() approach is broken though, because it's easy to imagine cases
like where some foreign object is passed to a function, and the
function checks the type with is().

I can change is() to use the calling package as the fallback, so
DataFrame(1:5) no longer produces a message. But calling it from
another package, or global env, will still break, just like new(). How
does that sound?

On the other hand, maybe we should be more careful with calls to is()
and use class objects. That's a good workaround in this case, anyway,
since I probably can't get the change into R before release.

Michael


On Thu, Apr 12, 2018 at 9:03 AM, Aaron Lun 
> wrote:
Well, it's not really SingleCellExperiment's problem, either.

library(S4Vectors)
DataFrame(1:5) # Silent, okay.
library(RNeXML)
DataFrame(1:5) # Prints out the message
## Found more than one class "Annotated" in cache; using the first,
from namespace 'S4Vectors'
## Also defined by ‘RNeXML’

Session information attached below.

-Aaron

sessionInfo()
R Under development (unstable) (2018-03-26 r74466)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: 
/home/cri.camres.org/lun01/Software/R/trunk/lib/libRblas.so
LAPACK: 
/home/cri.camres.org/lun01/Software/R/trunk/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8   LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41
[4] BiocGenerics_0.25.3

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16compiler_3.6.0  pillar_1.2.1
[4] plyr_1.8.4  bindr_0.1.1 iterators_1.0.9
[7] tools_3.6.0 uuid_0.1-2  jsonlite_1.5
[10] tibble_1.4.2nlme_3.1-137lattice_0.20-35
[13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4
[16] crul_0.5.2  curl_3.2bindrcpp_0.2.2
[19] httr_1.3.1  stringr_1.3.0   dplyr_0.7.4
[22] xml2_1.2.0  grid_3.6.0  reshape_0.8.7
[25] glue_1.2.0  data.table_1.10.4-3 R6_2.2.2
[28] XML_3.98-1.10   purrr_0.2.4 reshape2_1.4.3
[31] tidyr_0.8.0 magrittr_1.5codetools_0.2-15
[34] assertthat_0.2.0bold_0.5.0  taxize_0.9.3
[37] stringi_1.1.7   lazyeval_0.2.1  zoo_1.8-1


On Thu, 2018-04-12 at 17:40 +0200, Elizabeth Purdom wrote:
Just to follow up on my previous post. I am able to replicate the
problem in the problem like in the github post from 2 years ago (http
s://github.com/epurdom/clusterExperiment/issues/66
)
 only now it
is not the SummarizedExperiment class but the SingleCellExperiment
class that has the problem. [And I was incorrect, the problem does
occur in  development version 2018-03-22 r74446].

So this is actually a problem with the SingleCellExperiment package —
sorry for the incorrect subject line.

All of the best,
Elizabeth



library(SingleCellExperiment)
SingleCellExperiment()
class: SingleCellExperiment
dim: 0 0

Re: [Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

[Shepherd, Lori]

Generally this means that there are multiple locations where the package is 
installed - as determined by .libPaths() -


The single package builder specifies a package specific place to install 
packages that are not installed by the daily builder

C:/Users/pkgbuild/packagebuilder/workers/jobs/704/R-libs


The package that was installled in this directory was masking the version used 
by the default location -


This is an issue on our end and if it occurs you should notify a Bioconductor 
team member.




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 Paul Shannon 

Sent: Tuesday, April 10, 2018 7:25:54 PM
To: bioc-devel
Subject: [Bioc-devel] right version "masked" by wrong version - not sure what 
"masked means"

I am trying to build IGV (a new submission) on windows (tokay2) after linux and 
macOS build clean.

IGV needs its base class package, BrowserViz, at version >= 2.0, whose build 
report is OK for install, build, and build bin.   BrowserViz 2.0.11 fails 
check, probably because now web browser is available on the build machines.

The IGV build on windows reports an error I have not seen before.  Can anyone 
help?  What does �masked� mean in this context - not of a function, method or 
variable, but apparently of the entire package?

- Paul

* installing *source* package 'IGV' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: version 2.0.11 of 'BrowserViz' masked by 1.11.0 in 
C:/Users/pkgbuild/packagebuilder/workers/jobs/704/R-libs
Error : package 'BrowserViz' 1.11.0 was found, but >= 2.0 is required by 'IGV'

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[Bioc-devel] Workflow Package Updates / Guidelines

[Shepherd, Lori]

As mentioned before the workflows are in git and are now building on our
standard build machines.

The build reports are generated mon, wed, fri and can be seen here
http://bioconductor.org/checkResults/3.7/workflows-LATEST/

Moving forward we want to align how we treat workflows with how we treat the
software and data experiment packages.

Some of this can already be seen on the biocViews section of the website
http://bioconductor.org/packages/devel/BiocViews.html#___Workflow
You'll notice we started adding specific Workflow biocViews terms based on the
categories that were used on the http://bioconductor.org/help/workflows/ page.
We have updated the workflow packages to include appropriate biocViews from this
page as well. The updated biocViews are already updated in the Bioconductor
git.bioconductor.org repositories and should be reflected on the website after
monday's build of the workflows. If anyone thinks additional workflow views
would be helpful please email lori.sheph...@roswellpark.org or post for
discussion on our community workflow slack feed
https://community-bioc.slack.com/messages/CA17HQDGE/convo/CA17HQDGE-1522768000.000477/


 Eventually, the http://bioconductor.org/help/workflows/ will be retired, as the
 workflows now have a standard landing page (linked off the biocViews page
 above). We will be adding redirects internally to hopefully protect any
 existing links in papers and such.

 Moving forward we will have a few additional requires for the  vignettes of
 workflow packages.  Namely that the  vignette has a meaningful name  and that
 it uses BiocStyle for formatting. This is an effort to standardize the
 workflows. Currently we will enforce  BiocStyle::html_document.  We are in  the
 works of developing a html_workflow_template. We encourage any vignettes that
 are not using this BiocStyle format to update the workflow vignette as soon as
 possible - eventually this update will be required.

Keep in mind also - that a proper version bump will be needed to trigger build
and propagation of workflows. And since the workflows will be building on
release and devel they should follow the similar guidelines regarding versioning
http://bioconductor.org/developers/how-to/version-numbering/

We welcome any feedback

Cheers,




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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Re: [Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

[Paul Shannon]

Thanks, Lori.  The package masking problem went away a few days ago.

 - Paul

> On Apr 13, 2018, at 10:31 AM, Shepherd, Lori  
> wrote:
> 
> Generally this means that there are multiple locations where the package is 
> installed - as determined by .libPaths() - 
> 
> The single package builder specifies a package specific place to install 
> packages that are not installed by the daily builder
> C:/Users/pkgbuild/packagebuilder/workers/jobs/704/R-libs
> 
> The package that was installled in this directory was masking the version 
> used by the default location - 
> 
> This is an issue on our end and if it occurs you should notify a Bioconductor 
> team member. 
> 
> 
> 
> 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 Paul Shannon 
> 
> Sent: Tuesday, April 10, 2018 7:25:54 PM
> To: bioc-devel
> Subject: [Bioc-devel] right version "masked" by wrong version - not sure what 
> "masked means"
>  
> I am trying to build IGV (a new submission) on windows (tokay2) after linux 
> and macOS build clean.
> 
> IGV needs its base class package, BrowserViz, at version >= 2.0, whose build 
> report is OK for install, build, and build bin.   BrowserViz 2.0.11 fails 
> check, probably because now web browser is available on the build machines.
> 
> The IGV build on windows reports an error I have not seen before.  Can anyone 
> help?  What does “masked” mean in this context - not of a function, method or 
> variable, but apparently of the entire package?
> 
> - Paul
> 
> * installing *source* package 'IGV' ...
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Warning: version 2.0.11 of 'BrowserViz' masked by 1.11.0 in 
> C:/Users/pkgbuild/packagebuilder/workers/jobs/704/R-libs
> Error : package 'BrowserViz' 1.11.0 was found, but >= 2.0 is required by 'IGV'
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
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> e-mail and delete this email message from your computer. Thank you. 

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Re: [Bioc-devel] TIMEOUT on package MEAL

[Carlos Ruiz]

Hi BiocDevel,

Could you help me with this issue? The report is not very informative. I 
suspect that the vignettes are taking too long but I have two vignettes 
and I don't know which one is more problematic. I don't understand 
either why I have a timeout in OS and Linux but not in Windows.


When I had to deal with warnings or errors, I was able to reproduce them 
in my computer and solve them. Is there any way to reproduce the timeouts?


Thank you,

Carlos Ruiz


El 12/04/2018 a las 18:22, Turaga, Nitesh escribió:

Dear maintainer,

I'd like to bring to your attention that the  your package is getting a TIMEOUT 
'R CMD build' on platforms in the devel version of Bioconductor (i.e. BioC 3.7):

http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.html

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
mailing list if you have any question or need help.

The package is failing on devel which is very problematic. If it is not fixed 
in devel in a timely manner we would also consider this package for potential 
deprecation in the next cycle.  The deadline for passing R CMD build and check 
in devel is April 25.

Thanks for your contribution to Bioconductor.

Pleae be advised that Bioconductor has switched from svn to Git. Some helpful
links can be found here:
https://bioconductor.org/developers/how-to/git/

Best,

Nitesh Turaga
Bioconductor Core Team

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--
Carlos Ruiz
PhD Student
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Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 7309
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Re: [Bioc-devel] commit not appearing in report

[Shepherd, Lori]

version  0.99.22  is what is in the git.bioconductor.org repository -


It can take up to 24 hours from when you commit to see it reflected on the 
build report

http://bioconductor.org/checkResults/3.7/bioc-LATEST/



Note:  This is still yesterday's build report -  today's should be up very soon 
-

Please check back when today's report is up - it should reflect your changes.




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 Nicolas 
Descostes 
Sent: Friday, April 13, 2018 9:52:13 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] commit not appearing in report

Dear Community,

I have done a commit the 11th of April that does not appear anywhere. My
package is ChIPSeqSpike and the last push should be 0.99.22.

The build report indicates:

*ChIPSeqSpike
 0.99.21*
Nicolas Descostes
Last Commit: 026abdf
Last Changed Date: 2018-03-07 16:42:59 -0400

I have run the following commands:

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git log
commit 8a73abfd89db3af973f3f9d55283571451811ea9
Author: descostes 
Date:   Wed Apr 11 17:08:15 2018 -0400

Corrected bug in object constructor


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

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git diff
descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$


I did not run the following commands as I am not sure that this could erase
my modifications:

BiocGenerics$ git checkout master
BiocGenerics$ git pull



Any suggestions?

Thank you,

Nicolas

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[Bioc-devel] commit not appearing in report

[Nicolas Descostes]

Dear Community,

I have done a commit the 11th of April that does not appear anywhere. My
package is ChIPSeqSpike and the last push should be 0.99.22.

The build report indicates:

*ChIPSeqSpike
 0.99.21*
Nicolas Descostes
Last Commit: 026abdf
Last Changed Date: 2018-03-07 16:42:59 -0400

I have run the following commands:

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git log
commit 8a73abfd89db3af973f3f9d55283571451811ea9
Author: descostes 
Date:   Wed Apr 11 17:08:15 2018 -0400

Corrected bug in object constructor


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

descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$ git diff
descostes@reinbergLab:~/git/bioconductor/ChIPSeqSpike$


I did not run the following commands as I am not sure that this could erase
my modifications:

BiocGenerics$ git checkout master
BiocGenerics$ git pull



Any suggestions?

Thank you,

Nicolas

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Re: [Bioc-devel] Need some help to submit a R package.

[Pijush Das]

Dear Sir,


I have submitted an R package named "sigFeature" in Github and also
Bioconductor 9 days before.
The reviewers only said that there is some WARNING problem in the package
in different platform.

But after that they are not communicating any thing regarding the package.
I have checked the package
windows and Ubuntu it is working fine.

I unable to understand what actually the problem is ?
And the reviewers are not communicating about the problem. Though I am
getting lots of email from bioc-devel dealing with others package
problem .

Please suggest me what should I do now ?




Thank you



Regards
Pijush




On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> Please read through this documentation.
>
> http://bioconductor.org/developers/package-submission/
>
>
> Nitesh
>
> > On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:
> >
> > Dear Sir,
> >
> >
> >
> > I have developed an R package. I want to submit this package in
> > Bioconductor.
> > Please help me to submit the R package.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > regards
> > Pijush Das
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

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