[R-pkg-devel] Indexing HTML vignette topics

[Lenth, Russell V]

Developers,

I have a package that has a number of vignettes with examples and such; so I 
see an increasing need to provide easier ways to navigate among them and to 
find a particular topic. All the vignettes are written using R Markdown, 
subsequently converted to HTML. 

I did some searching but did not find software that would help (though I'm sure 
if it exists, I'm about to hear about it). So, in case anybody is interested, I 
threw together a small R package named vigindex for this purpose, and it is 
available on github at https://github.com/rvlenth/vigindex.

It works by inserting HTML comments in the vignette .Rmd files of the form:



and then running vigindex::vigindex(). This compiles all the index entries in 
the files in the vignette directory, and creates a new .Rmd file with the 
index. Each index entry is linked to the nearest section preceding each 
embedded entry. There are various refinements to allow for formatting and 
sorting.

There is an example vignette in the package, and the latest commit of 
https://github.com/rvlenth/emmeans has a topical index of all of its vignettes.

I'm interested in any comments or suggestions, and if anybody finds this useful.

Russ
--
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Department of Statistics and Actuarial Science   
The University of Iowa  -  Iowa City, IA 52242  USA   
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Re: [Bioc-devel] git push confusion

[Hervé Pagès]

Hi Karl,

We don't have an easy way to know when exactly you pushed your changes
to git.bioconductor.org but it seems that you did it only today so you
need to wait about 24h to see this reflected on the build report.

H.

On 04/23/2018 09:26 AM, Turaga, Nitesh wrote:

You can check which version is being used by going to this link

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_rgsepd_malbec2-2Dbuildsrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-Ng=STBZLhkw4xWhHtcRjR0pqgICNEPwujMXtkiAWkcKoe0=

It seems that your package is using the commit from Oct 30th. We’ll take a look at this, it seems to be 
an issue with the build system. Your Bioconductor git server is up to date though, you can see if you 
commit posted by taking a look at our log 
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_gitlog_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-Ng=De6-RIOuVqDeKOJbsyThMPIz7ZNegINb7haUTl8XuFc=
 or subscribing to our feed.


Best,

Nitesh




On Apr 23, 2018, at 12:19 PM, Karl Stamm  wrote:

I did all that. git push upstream master says "everything up to date" and step 
7 says confirm the changes by browsing Github.
Github.org has had the changes since Friday but the build servers did not have the 
changes when the build was attempted on Sunday.  Are they on a branch other than 
"master"? How can I tell what the build servers are using ?

On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh 
 wrote:
Please check out the documentation

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_push-2Dto-2Dgithub-2Dbioc_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-Ng=6T2m63ST5D4aYpOTH1eh7nHJt6Ic5BrCT3AEg1uodWA=


On Apr 23, 2018, at 12:13 PM, Karl Stamm  wrote:

How do I "push to both"? I dont understand the numerous git terminology. On 
Friday I tried to push the bugfix but the build server still errors.
git log
commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master, 
upstream/master, origin/master, origin/HEAD)

So I guess the build servers are not "upstream/master" ??

I have this setup as given in the bioconductor documentation
git remote -v
origing...@github.com:kstammits/rgsepd.git (fetch)
origing...@github.com:kstammits/rgsepd.git (push)
upstream  g...@git.bioconductor.org:packages/rgsepd.git (fetch)
upstream  g...@git.bioconductor.org:packages/rgsepd.git (push)


And when I do various push commands they say "everything up to date"
But I want to make sure the bioc servers get the update before the 3.7 
lockdown. Is there any way to see what the are holding ?





On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh 
 wrote:
Hi Karl,

Bioconductor doesn’t automatically grab changes from your Github. A large body 
of the work is maintained only on our Bioconductor git server. The maintainer 
has to push to both Github and the Bioconductor server if the changes have to 
propagate.

RELEASE_3_6 is now frozen forever. We announced this on April 11th. You cannot 
push to this anymore. You can still make your changes on your master branch.

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013212.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-Ng=P9oxAe7ZO_iYe2Q7bRf6AzXrSLZCjuKK928OwvRKE0A=

Best,

Nitesh





On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:

I got a message this morning that malbec2 has build errors on my package.
It's a bug I fixed a few days ago, but it looks like I didn't push changes
to the right branches or something.  How do I get the bioc systems to take
from the github updates?
The help documents on the bioconductor website say to push to RELEASE_3_6
but that doesn't seem to work. And the build server is running the previous
code version, but calling it 3.7.
I'm not sure they've gotten my changes, how can i see which versions the
build servers have? Seems they do not automatically grab from github since
the bug was fixed a few days ago there.

   [[alternative HTML version deleted]]

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

[Hervé Pagès]

Completely agree on the importance of disambiguating class references
in the long term.

However I still think that just because we have a mechanism to
disambiguate means we shouldn't make an effort to avoid name clashes,
especially when the name clash is easy to avoid, like in the case
discussed here. Annotated is not a good name anyway. Something like
Annotatable would be more appropriate. Objects of this class **can**
be annotated but many of them are not.

H.

On 04/14/2018 12:25 PM, Michael Lawrence wrote:

Last night I checked in a workaround to S4Vectors. It just calls
getClass("Annotated") instead of passing the class name directly.

I'll check in a simple fix for is() today maybe to R 3.6 (devel) and
then we'll be good for now.

On Sat, Apr 14, 2018 at 8:59 AM, Martin Morgan
 wrote:

On 04/14/2018 07:21 AM, Vincent Carey wrote:


But Annotated is defined in S4Vectors and RNeXML; the latter is not a
Bioconductor package.

The likelihood of collisions among class names defined in different
packages seems pretty high
as S4 adoption grows.  So requiring a systematic approach to
disambiguating
class references seems inevitable.



I agree that renaming is not a robust solution, and would encourage Michael
to commit the change using the class definition in `is()` with more
elaborate solutions (really this is a problem with is(), where it should be
fixed, rather than introducing complicated syntax?) left for a later day.

Martin




On Sat, Apr 14, 2018 at 4:05 AM, Hervé Pagès  wrote:


How about renaming Annotated? Isn't having 2 classes around with the
same name fundamentally a bad situation? No amount of workarounds will
change that.

H.


On 04/12/2018 04:06 PM, Michael Lawrence wrote:


Yea, good idea, I was thinking of supporting :: in class names and
parsing them out. In code is better.  Maybe %::%? It wouldn't have to
get a class object (for one thing, a class might not exist), because
the methods package supports a 'package' attribute on the character
vector, abstracted by packageSlot().



On Thu, Apr 12, 2018 at 3:26 PM, Vincent Carey
 wrote:


If we need to disambiguate class references, perhaps an operator

could help?  Along the lines of base::"::" ...


"%c%" <- function(package,class) {

  pk = as.character(substitute(package))

  cl = as.character(substitute(class))

  getClass(cl, where=getNamespace(pk))

}


Biobase %c% ExpressionSet  # a classRepresentation instance


is(1:5, Biobase %c% ExpressionSet)  # FALSE


is(Biobase::ExpressionSet(), "ExpressionSet")  # TRUE


is(Biobase::ExpressionSet(),  Biobase %c% ExpressionSet) # TRUE






On Thu, Apr 12, 2018 at 3:57 PM, Michael Lawrence
 wrote:



Hi Davide,

We can get this fixed soon, but I was hoping to hear e.g. Herve's
opinion first if he has one.

Michael

On Thu, Apr 12, 2018 at 12:53 PM, Davide Risso

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)

Re: [Bioc-devel] I could't push My package GMRP to github/master

[Turaga, Nitesh]

Hi Yuande,

Please try to follow the commands on the documentation line by line. 

http://bioconductor.org/developers/how-to/git/maintain-github-bioc/

Follow these instructions as is, and please send me the output of each command. 

Best,

Nitesh 

> On Apr 23, 2018, at 7:53 PM, Yuande Tan  wrote:
> 
> Hi Turraga,
> Thank you so much for helping me to push MBttest to Bioconductor.
> I have addressed problem in another package GMRP and everything is OK when I 
> ran R CMD check and build. I also created repository GMRP in my github 
> account.
> But I could not push the package GMRP in my local computer to github master, 
> the problem is
> git push  origin g...@git.bioconductor.org:packages/GMRP/master
> error: src refspec g...@git.bioconductor.org does not match any.
> error: failed to push some refs to'g...@git.bioconductor.org:packages/GMRP'
> 
> I tried to address this problem by following google's answers.
> But I was failed to do push.
> 
> I need your help again.
> 
> I am looking forward to hear you.
> 
> Sincerely
> 
> Yuande 
> 



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Re: [Bioc-devel] Unable to push to origin master

[Turaga, Nitesh]

I’d have to investigate a little more. But maybe someone else on the community 
might have some more insight. 

Best,

Nitesh 


> On Apr 23, 2018, at 7:26 PM, Giorgio Melloni  
> wrote:
> 
> No I only get the error on GitHub but not on on Bioconductor upstream. I 
> guess it’s not that important but in case others have the same problem it 
> would be nice to know.
> 
> Giorgio
> 
>> On Apr 23, 2018, at 19:18, Turaga, Nitesh  
>> wrote:
>> 
>> Hi Giorgio,
>> 
>> This is an issue with Github. They have a pre-receive hook on Github’s end 
>> which is being triggered. Do you get the same error message when you push to 
>> Bioconductor (upstream)? (git push upstream master)
>> 
>> I’m not sure why you are getting an error with that .rb (ruby) extension.
>> 
>> Your remotes are set up correct.  
>> 
>> Best,
>> 
>> Nitesh 
>> 
>> 
>>> On Apr 16, 2018, at 2:10 PM, Giorgio Melloni  
>>> wrote:
>>> 
>>> Dear Bioc-Devel,
>>> 
>>> I’ve just updated my package for the upcoming release upstream successfully 
>>> using "git push upstream master”.
>>> My current remotes are set to:
>>> 
>>> origin  https://github.com/gmelloni/LowMACA.git (fetch)
>>> origin  https://github.com/gmelloni/LowMACA.git (push)
>>> upstreamg...@git.bioconductor.org:packages/LowMACA.git (fetch)
>>> upstreamg...@git.bioconductor.org:packages/LowMACA.git (push)
>>> 
>>> 
>>> When I try to do the same to origin (git push origin master) I receive the 
>>> following error:
>>> 
>>> Counting objects: 18, done.
>>> Delta compression using up to 8 threads.
>>> Compressing objects: 100% (16/16), done.
>>> Writing objects: 100% (18/18), 8.16 KiB | 2.72 MiB/s, done.
>>> Total 18 (delta 8), reused 0 (delta 0)
>>> remote: Resolving deltas: 100% (8/8), completed with 6 local objects.
>>> remote: 
>>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>>>  `ip': getaddrinfo: Name or service not known (SocketError)
>>> remote: from 
>>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>>>  `initialize'
>>> remote: from 
>>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>>>  `new'
>>> remote: from 
>>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>>>  `add_shard'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `block in 
>>> create_statsd'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `each'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in 
>>> `create_statsd'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:20:in `stats'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:244:in 
>>> `'
>>> remote: from 
>>> /data/github/releases/deploy-b/lib/github/config/stats.rb:12:in `>> (required)>'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/lib/github/logger.rb:3:in 
>>> `'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/lib/github.rb:137:in 
>>> `'
>>> remote: from /data/github/releases/deploy-b/lib/github.rb:20:in `>> (required)>'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:66:in 
>>> `require'
>>> remote: from /data/github/releases/deploy-b/config/basic.rb:230:in 
>>> `'
>>> remote: from 
>>> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>>>  `require'
>>> remote: from 
>>> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>>>  `require'
>>> To https://github.com/gmelloni/LowMACA.git
>>> ! [remote rejected] master -> master (pre-receive hook declined)
>>> error: failed to push some refs to 'https://github.com/gmelloni/LowMACA.git’
>>> 
>>> I’ve probably set up the remotes in the wrong way. Any help is appreciated.
>>> 
>>> thanks
>>> 
>>> Giorgio
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
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Re: [Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

[Hervé Pagès]

Hi Paul,

trena imports RMySQL and RPostgreSQL. Both packages define and export
dbApply() so by importing all the symbols from both packages you get a
name clash. You can get around this by importing only the things you
need. It seems that you only call the following generic functions in
trena:

  dbConnect
  dbListTables
  dbGetQuery
  dbListConnections
  dbDisconnect

These are S4 generic functions that are defined in the DBI package so
they should be imported from there. Also import the corresponding
methods defined in RMySQL and RPostgreSQL. Your NAMESPACE file will
look something like this:

importFrom(DBI,
dbConnect,
dbListTables,
dbGetQuery,
dbListConnections,
dbDisconnect)


importMethodsFrom(RMySQL,
dbConnect,
dbListTables,
dbGetQuery,
dbListConnections,
dbDisconnect)

importMethodsFrom(RPostgreSQL,
dbConnect,
dbListTables,
dbGetQuery,
dbListConnections,
dbDisconnect)

BTW have you considered using RMariaDB instead of RMySQL?

  https://cran.r-project.org/web/packages/RMariaDB/

Cheers,
H.

On 04/23/2018 11:12 AM, Paul Shannon wrote:


 Warning: replacing previous import ‘RMySQL::dbApply’ by 
‘RPostgreSQL::dbApply’ when loading ‘trena’

We do not call dbApply directly anywhere in the package. I imagine it is called 
routinely by functions that we do call.

Any suggestions on how to clear this warning?

Thanks.

  - Paul

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Program in Computational Biology
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E-mail: hpa...@fredhutch.org
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Fax:(206) 667-1319

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Re: [Bioc-devel] Unable to push to origin master

[Turaga, Nitesh]

Hi Giorgio,

This is an issue with Github. They have a pre-receive hook on Github’s end 
which is being triggered. Do you get the same error message when you push to 
Bioconductor (upstream)? (git push upstream master)

I’m not sure why you are getting an error with that .rb (ruby) extension.

 Your remotes are set up correct.  

Best,

Nitesh 


> On Apr 16, 2018, at 2:10 PM, Giorgio Melloni  
> wrote:
> 
> Dear Bioc-Devel,
> 
> I’ve just updated my package for the upcoming release upstream successfully 
> using "git push upstream master”.
> My current remotes are set to:
> 
> originhttps://github.com/gmelloni/LowMACA.git (fetch)
> originhttps://github.com/gmelloni/LowMACA.git (push)
> upstream  g...@git.bioconductor.org:packages/LowMACA.git (fetch)
> upstream  g...@git.bioconductor.org:packages/LowMACA.git (push)
> 
> 
> When I try to do the same to origin (git push origin master) I receive the 
> following error:
> 
> Counting objects: 18, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (16/16), done.
> Writing objects: 100% (18/18), 8.16 KiB | 2.72 MiB/s, done.
> Total 18 (delta 8), reused 0 (delta 0)
> remote: Resolving deltas: 100% (8/8), completed with 6 local objects.
> remote: 
> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>  `ip': getaddrinfo: Name or service not known (SocketError)
> remote:   from 
> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>  `initialize'
> remote:   from 
> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>  `new'
> remote:   from 
> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>  `add_shard'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `block in 
> create_statsd'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `each'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in 
> `create_statsd'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:20:in `stats'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:244:in 
> `'
> remote:   from 
> /data/github/releases/deploy-b/lib/github/config/stats.rb:12:in ` (required)>'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/lib/github/logger.rb:3:in 
> `'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/lib/github.rb:137:in 
> `'
> remote:   from /data/github/releases/deploy-b/lib/github.rb:20:in ` (required)>'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:66:in 
> `require'
> remote:   from /data/github/releases/deploy-b/config/basic.rb:230:in 
> `'
> remote:   from 
> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>  `require'
> remote:   from 
> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>  `require'
> To https://github.com/gmelloni/LowMACA.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'https://github.com/gmelloni/LowMACA.git’
> 
> I’ve probably set up the remotes in the wrong way. Any help is appreciated.
> 
> thanks
> 
> Giorgio
> 
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Re: [Bioc-devel] Unable to push to origin master

[Giorgio Melloni]

No I only get the error on GitHub but not on on Bioconductor upstream. I guess 
it’s not that important but in case others have the same problem it would be 
nice to know.

Giorgio

> On Apr 23, 2018, at 19:18, Turaga, Nitesh  
> wrote:
> 
> Hi Giorgio,
> 
> This is an issue with Github. They have a pre-receive hook on Github’s end 
> which is being triggered. Do you get the same error message when you push to 
> Bioconductor (upstream)? (git push upstream master)
> 
> I’m not sure why you are getting an error with that .rb (ruby) extension.
> 
> Your remotes are set up correct.  
> 
> Best,
> 
> Nitesh 
> 
> 
>> On Apr 16, 2018, at 2:10 PM, Giorgio Melloni  
>> wrote:
>> 
>> Dear Bioc-Devel,
>> 
>> I’ve just updated my package for the upcoming release upstream successfully 
>> using "git push upstream master”.
>> My current remotes are set to:
>> 
>> origin   https://github.com/gmelloni/LowMACA.git (fetch)
>> origin   https://github.com/gmelloni/LowMACA.git (push)
>> upstream g...@git.bioconductor.org:packages/LowMACA.git (fetch)
>> upstream g...@git.bioconductor.org:packages/LowMACA.git (push)
>> 
>> 
>> When I try to do the same to origin (git push origin master) I receive the 
>> following error:
>> 
>> Counting objects: 18, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (16/16), done.
>> Writing objects: 100% (18/18), 8.16 KiB | 2.72 MiB/s, done.
>> Total 18 (delta 8), reused 0 (delta 0)
>> remote: Resolving deltas: 100% (8/8), completed with 6 local objects.
>> remote: 
>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>>  `ip': getaddrinfo: Name or service not known (SocketError)
>> remote:  from 
>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:23:in
>>  `initialize'
>> remote:  from 
>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>>  `new'
>> remote:  from 
>> /data/github/releases/deploy-b/vendor/gems/2.4.2/ruby/2.4.0/gems/statsd-ruby-0.3.0.github.3.38.gd478cc7/lib/github/statsd.rb:106:in
>>  `add_shard'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `block in 
>> create_statsd'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in `each'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:33:in 
>> `create_statsd'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:20:in `stats'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:244:in 
>> `'
>> remote:  from 
>> /data/github/releases/deploy-b/lib/github/config/stats.rb:12:in `> (required)>'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/lib/github/logger.rb:3:in 
>> `'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/lib/github.rb:137:in 
>> `'
>> remote:  from /data/github/releases/deploy-b/lib/github.rb:20:in `> (required)>'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:66:in 
>> `require'
>> remote:  from /data/github/releases/deploy-b/config/basic.rb:230:in 
>> `'
>> remote:  from 
>> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>>  `require'
>> remote:  from 
>> /data/github/releases/deploy-b/vendor/ruby/44c51a28900fc53699489c87289294b79ee365d3/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in
>>  `require'
>> To https://github.com/gmelloni/LowMACA.git
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 'https://github.com/gmelloni/LowMACA.git’
>> 
>> I’ve probably set up the remotes in the wrong way. Any help is appreciated.
>> 
>> thanks
>> 
>> Giorgio
>> 
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> 
> 
> 
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> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
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> 

[Rd] Bug 16719: kruskal.test documentation for formula

[Thomas Levine]

I submit a couple options for addressing bug 16719: kruskal.test
documentation for formula.
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16719

disallow-character.diff changes the documentation and error message
to indicate that factors are accepted.

allow-character.diff changes the kruskal.test functions to convert
character vectors to factors; documentation is updated accordingly.

I tested the updated functions with the examples in example.R. It is
based on the examples in the bug report.

If there is interest in applying either patch, especially the latter,
I want first to test the change on lots of existing programs that call
kruskal.test, to see if it causes any regressions. Is there a good place
to look for programs that use particular R functions?

I am having trouble building R, so I have so far tested these changes
only by patching revision 74631 (SVN head) and sourcing the resulting
kruskal.test.R in R 3.4.1 on OpenBSD 6.2. I thus have not tested the
R documentation files.
Index: src/library/stats/R/kruskal.test.R
===
--- src/library/stats/R/kruskal.test.R  (revision 74631)
+++ src/library/stats/R/kruskal.test.R  (working copy)
@@ -46,7 +46,10 @@
 x <- x[OK]
 g <- g[OK]
 if (!all(is.finite(g)))
-stop("all group levels must be finite")
+if (is.character(g))
+stop("all group levels must be finite; convert group to a 
factor")
+else
+stop("all group levels must be finite")
 g <- factor(g)
 k <- nlevels(g)
 if (k < 2L)
Index: src/library/stats/man/kruskal.test.Rd
===
--- src/library/stats/man/kruskal.test.Rd   (revision 74631)
+++ src/library/stats/man/kruskal.test.Rd   (working copy)
@@ -22,11 +22,12 @@
   \item{x}{a numeric vector of data values, or a list of numeric data
 vectors.  Non-numeric elements of a list will be coerced, with a
 warning.}
-  \item{g}{a vector or factor object giving the group for the
+  \item{g}{a numeric vector or factor object giving the group for the
 corresponding elements of \code{x}.  Ignored with a warning if
 \code{x} is a list.}
   \item{formula}{a formula of the form \code{response ~ group} where
-\code{response} gives the data values and \code{group} a vector or
+\code{response} gives the data values and \code{group}
+a numeric vector or
 factor of the corresponding groups.} 
   \item{data}{an optional matrix or data frame (or similar: see
 \code{\link{model.frame}}) containing the variables in the
@@ -52,7 +53,8 @@
   list, use \code{kruskal.test(list(x, ...))}.
 
   Otherwise, \code{x} must be a numeric data vector, and \code{g} must
-  be a vector or factor object of the same length as \code{x} giving
+  be a numeric vector or factor object of the same length as \code{x}
+  giving
   the group for the corresponding elements of \code{x}.
 }
 \value{
Index: src/library/stats/R/kruskal.test.R
===
--- src/library/stats/R/kruskal.test.R  (revision 74631)
+++ src/library/stats/R/kruskal.test.R  (working copy)
@@ -45,7 +45,7 @@
 OK <- complete.cases(x, g)
 x <- x[OK]
 g <- g[OK]
-if (!all(is.finite(g)))
+if (!is.character(g) & !all(is.finite(g)))
 stop("all group levels must be finite")
 g <- factor(g)
 k <- nlevels(g)
Index: src/library/stats/man/kruskal.test.Rd
===
--- src/library/stats/man/kruskal.test.Rd   (revision 74631)
+++ src/library/stats/man/kruskal.test.Rd   (working copy)
@@ -22,11 +22,13 @@
   \item{x}{a numeric vector of data values, or a list of numeric data
 vectors.  Non-numeric elements of a list will be coerced, with a
 warning.}
-  \item{g}{a vector or factor object giving the group for the
+  \item{g}{a character vector, numeric vector, or factor
+giving the group for the
 corresponding elements of \code{x}.  Ignored with a warning if
 \code{x} is a list.}
   \item{formula}{a formula of the form \code{response ~ group} where
-\code{response} gives the data values and \code{group} a vector or
+\code{response} gives the data values and \code{group} a
+character vector, numeric vector, or
 factor of the corresponding groups.} 
   \item{data}{an optional matrix or data frame (or similar: see
 \code{\link{model.frame}}) containing the variables in the
@@ -52,7 +54,8 @@
   list, use \code{kruskal.test(list(x, ...))}.
 
   Otherwise, \code{x} must be a numeric data vector, and \code{g} must
-  be a vector or factor object of the same length as \code{x} giving
+  be a numeric vector, character vector, or factor of the same length
+  as \code{x} giving
   the group for the corresponding elements of \code{x}.
 }
 \value{

Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Duncan Murdoch]

On 23/04/2018 12:28 PM, Peter Simons wrote:

Hi Dirk,

  > I have been doing for R for about 20 years (if you count the time I
  > assisted Doug Bates when he was still the maintainer) (and longer for
  > Debian), and you seem to follow the same model we set up years ago of
  > splitting the content of r-recommended (itself a virtual package) off
  > r-base-core.
  >
  > You simply need to do this in stages.

I have packaged free software for 20+ years for many different distributions,
and, in fact, I'm doing that professionally these days as an employee of one of
the largest commercial Linux distributors. So please trust my expertise when I
tell you that this is not what I want.

What I want is

   ./configure --without-recommended-packages && make && make check

to succeed without error, and I don't think that's an unreasonable expectation.


So you're getting paid to do what you do, but you want the volunteers in 
R Core to do some work for you for free.  I *do* think that's an 
unreasonable expectation.




I have reported these kind of errors before in past, and back then a friendly R
developer simply took a moment to disable the offending tests when the build
was configured with this particular flag and that solved the problem. I would
hope that this is the outcome we can achieve this time, too.


Perhaps back then you were also a volunteer.



If no-one wants to make those changes for whatever reason, then that's fine and
I'll just disable the test suite in NixOS to make the build succeed. I feel like
that would be a sub-optimal solution, though.


I agree.  You should spend some time working out a better one.

Duncan Murdoch

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[Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

[Paul Shannon]

Warning: replacing previous import ‘RMySQL::dbApply’ by 
‘RPostgreSQL::dbApply’ when loading ‘trena’

We do not call dbApply directly anywhere in the package. I imagine it is called 
routinely by functions that we do call.

Any suggestions on how to clear this warning?

Thanks.

 - Paul

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Re: [Bioc-devel] Deadline for All Package Maintainers

[Shepherd, Lori]

Yes that is correct. the changes should be pushed to the devel 'master' branch.


When the release occurs next week the RELEASE_3_7 branch will be created from 
the current master branch.  Ideally the package ERRORs are solved before this 
happens to avoid you having to make changes on both the release and devel 
branches.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Joris Meys 
Sent: Monday, April 23, 2018 1:47:20 PM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Deadline for All Package Maintainers

Just for the record: This is the deadline for getting everything solved before 
the packages get incorporated into the 3.7 release, right? So we should now 
push only to the master (as the release_3_7 branch apparently doesn't exist 
yet)?

Cheers
Joris

On Mon, Apr 23, 2018 at 2:35 PM, Shepherd, Lori 
> wrote:
This is a reminder that the last day to pass R CMD build and R CMD check is 
this Wednesday April 25th.  Please update all package that are failing on the 
build reports by this time.


Software Packages:

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

Data Experiment Packages:

http://bioconductor.org/checkResults/3.7/data-experiment-LATEST/

Workflow Packages:

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



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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Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

---
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Re: [Bioc-devel] Deadline for All Package Maintainers

[Shepherd, Lori]

Yes that is correct.  Changes should still be pushed to the devel  'master'  
branch


After the release happens next week there will be a RELEASE_3_7 branch created 
from the current master branch so ideally we would like to have packages solved 
so that you would not have to make fixes in both release and devel.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Joris Meys 
Sent: Monday, April 23, 2018 1:47:20 PM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Deadline for All Package Maintainers

Just for the record: This is the deadline for getting everything solved before 
the packages get incorporated into the 3.7 release, right? So we should now 
push only to the master (as the release_3_7 branch apparently doesn't exist 
yet)?

Cheers
Joris

On Mon, Apr 23, 2018 at 2:35 PM, Shepherd, Lori 
> wrote:
This is a reminder that the last day to pass R CMD build and R CMD check is 
this Wednesday April 25th.  Please update all package that are failing on the 
build reports by this time.


Software Packages:

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

Data Experiment Packages:

http://bioconductor.org/checkResults/3.7/data-experiment-LATEST/

Workflow Packages:

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



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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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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--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

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Re: [Bioc-devel] Deadline for All Package Maintainers

[Joris Meys]

Just for the record: This is the deadline for getting everything solved
before the packages get incorporated into the 3.7 release, right? So we
should now push only to the master (as the release_3_7 branch apparently
doesn't exist yet)?

Cheers
Joris

On Mon, Apr 23, 2018 at 2:35 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> This is a reminder that the last day to pass R CMD build and R CMD check
> is this Wednesday April 25th.  Please update all package that are failing
> on the build reports by this time.
>
>
> Software Packages:
>
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/
>
> Data Experiment Packages:
>
> http://bioconductor.org/checkResults/3.7/data-experiment-LATEST/
>
> Workflow Packages:
>
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
>
> 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
> 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.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
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http://www.biowiskundedagen.ugent.be/

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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Dirk Eddelbuettel]

Peter,

I think we are on the same page, but there is little I can do for you here.
Ultimately you are asking R Core to do you a favor. More below.

On 23 April 2018 at 18:28, Peter Simons wrote:
| Hi Dirk,
| 
|  > I have been doing for R for about 20 years (if you count the time I
|  > assisted Doug Bates when he was still the maintainer) (and longer for
|  > Debian), and you seem to follow the same model we set up years ago of
|  > splitting the content of r-recommended (itself a virtual package) off
|  > r-base-core.
|  >
|  > You simply need to do this in stages.
| 
| I have packaged free software for 20+ years for many different distributions,
| and, in fact, I'm doing that professionally these days as an employee of one 
of
| the largest commercial Linux distributors. So please trust my expertise when I
| tell you that this is not what I want.
| 
| What I want is
| 
|   ./configure --without-recommended-packages && make && make check
| 
| to succeed without error, and I don't think that's an unreasonable 
expectation.

Sure. You "merely" have to get R Core to implement it for you.  Given that it
does not help them (they just build 'with recommended') and is not strictly
needed (it will pass in a second pass once you used the first pass to build
the recommended packages) it is a little hard to see how this 'nice to have'
item may bubble higher on anybody's priorities.  But the general rules is
that if and when well-written patches are submitted on topics where there is
agreement that a fix may help, then they are considered. So *you* could work
on this.
 
| I have reported these kind of errors before in past, and back then a friendly 
R
| developer simply took a moment to disable the offending tests when the build
| was configured with this particular flag and that solved the problem. I would
| hope that this is the outcome we can achieve this time, too.

R Core disabled tests in base R for you?  Hm. Are you sure?  Or are you by
chance confusing R Core with a random package maintainer (like myself) who
may have disabled a test?
 
| If no-one wants to make those changes for whatever reason, then that's fine 
and
| I'll just disable the test suite in NixOS to make the build succeed. I feel 
like
| that would be a sub-optimal solution, though.

You could comment it out now, and re-enable it once your package stack is
refilled.  Or you could make it 'make -k check' for now.

It's really under your control as it your build environment.

Dirk

-- 
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Re: [Bioc-devel] git push confusion

[Turaga, Nitesh]

You can check which version is being used by going to this link

http://bioconductor.org/checkResults/devel/bioc-LATEST/rgsepd/malbec2-buildsrc.html

It seems that your package is using the commit from Oct 30th. We’ll take a look 
at this, it seems to be an issue with the build system. Your Bioconductor git 
server is up to date though, you can see if you commit posted by taking a look 
at our log http://bioconductor.org/developers/gitlog/ or subscribing to our 
feed.


Best,

Nitesh 



> On Apr 23, 2018, at 12:19 PM, Karl Stamm  wrote:
> 
> I did all that. git push upstream master says "everything up to date" and 
> step 7 says confirm the changes by browsing Github.
> Github.org has had the changes since Friday but the build servers did not 
> have the changes when the build was attempted on Sunday.  Are they on a 
> branch other than "master"? How can I tell what the build servers are using ? 
> 
> On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh 
>  wrote:
> Please check out the documentation
> 
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
> 
> > On Apr 23, 2018, at 12:13 PM, Karl Stamm  wrote:
> > 
> > How do I "push to both"? I dont understand the numerous git terminology. On 
> > Friday I tried to push the bugfix but the build server still errors.
> > git log
> > commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master, 
> > upstream/master, origin/master, origin/HEAD)
> > 
> > So I guess the build servers are not "upstream/master" ?? 
> > 
> > I have this setup as given in the bioconductor documentation
> > git remote -v
> > origing...@github.com:kstammits/rgsepd.git (fetch)
> > origing...@github.com:kstammits/rgsepd.git (push)
> > upstream  g...@git.bioconductor.org:packages/rgsepd.git (fetch)
> > upstream  g...@git.bioconductor.org:packages/rgsepd.git (push)
> > 
> > 
> > And when I do various push commands they say "everything up to date"  
> > But I want to make sure the bioc servers get the update before the 3.7 
> > lockdown. Is there any way to see what the are holding ? 
> > 
> > 
> > 
> > 
> > 
> > On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh 
> >  wrote:
> > Hi Karl,
> > 
> > Bioconductor doesn’t automatically grab changes from your Github. A large 
> > body of the work is maintained only on our Bioconductor git server. The 
> > maintainer has to push to both Github and the Bioconductor server if the 
> > changes have to propagate. 
> > 
> > RELEASE_3_6 is now frozen forever. We announced this on April 11th. You 
> > cannot push to this anymore. You can still make your changes on your master 
> > branch. 
> > 
> > https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013212.html
> > 
> > Best,
> > 
> > Nitesh 
> > 
> > 
> > 
> > 
> > > On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:
> > > 
> > > I got a message this morning that malbec2 has build errors on my package.
> > > It's a bug I fixed a few days ago, but it looks like I didn't push changes
> > > to the right branches or something.  How do I get the bioc systems to take
> > > from the github updates?
> > > The help documents on the bioconductor website say to push to RELEASE_3_6
> > > but that doesn't seem to work. And the build server is running the 
> > > previous
> > > code version, but calling it 3.7.
> > > I'm not sure they've gotten my changes, how can i see which versions the
> > > build servers have? Seems they do not automatically grab from github since
> > > the bug was fixed a few days ago there.
> > > 
> > >   [[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.
> > 
> 
> 
> 
> 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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> received this message in error, please notify the sender immediately by 
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Re: [Bioc-devel] git push confusion

[Turaga, Nitesh]

Please check out the documentation

http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

> On Apr 23, 2018, at 12:13 PM, Karl Stamm  wrote:
> 
> How do I "push to both"? I dont understand the numerous git terminology. On 
> Friday I tried to push the bugfix but the build server still errors.
> git log
> commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master, 
> upstream/master, origin/master, origin/HEAD)
> 
> So I guess the build servers are not "upstream/master" ?? 
> 
> I have this setup as given in the bioconductor documentation
> git remote -v
> origing...@github.com:kstammits/rgsepd.git (fetch)
> origing...@github.com:kstammits/rgsepd.git (push)
> upstream  g...@git.bioconductor.org:packages/rgsepd.git (fetch)
> upstream  g...@git.bioconductor.org:packages/rgsepd.git (push)
> 
> 
> And when I do various push commands they say "everything up to date"  
> But I want to make sure the bioc servers get the update before the 3.7 
> lockdown. Is there any way to see what the are holding ? 
> 
> 
> 
> 
> 
> On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh 
>  wrote:
> Hi Karl,
> 
> Bioconductor doesn’t automatically grab changes from your Github. A large 
> body of the work is maintained only on our Bioconductor git server. The 
> maintainer has to push to both Github and the Bioconductor server if the 
> changes have to propagate. 
> 
> RELEASE_3_6 is now frozen forever. We announced this on April 11th. You 
> cannot push to this anymore. You can still make your changes on your master 
> branch. 
> 
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013212.html
> 
> Best,
> 
> Nitesh 
> 
> 
> 
> 
> > On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:
> > 
> > I got a message this morning that malbec2 has build errors on my package.
> > It's a bug I fixed a few days ago, but it looks like I didn't push changes
> > to the right branches or something.  How do I get the bioc systems to take
> > from the github updates?
> > The help documents on the bioconductor website say to push to RELEASE_3_6
> > but that doesn't seem to work. And the build server is running the previous
> > code version, but calling it 3.7.
> > I'm not sure they've gotten my changes, how can i see which versions the
> > build servers have? Seems they do not automatically grab from github since
> > the bug was fixed a few days ago there.
> > 
> >   [[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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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Peter Simons]

Hi Dirk,

 > I have been doing for R for about 20 years (if you count the time I
 > assisted Doug Bates when he was still the maintainer) (and longer for
 > Debian), and you seem to follow the same model we set up years ago of
 > splitting the content of r-recommended (itself a virtual package) off
 > r-base-core.
 >
 > You simply need to do this in stages.

I have packaged free software for 20+ years for many different distributions,
and, in fact, I'm doing that professionally these days as an employee of one of
the largest commercial Linux distributors. So please trust my expertise when I
tell you that this is not what I want.

What I want is

  ./configure --without-recommended-packages && make && make check

to succeed without error, and I don't think that's an unreasonable expectation.

I have reported these kind of errors before in past, and back then a friendly R
developer simply took a moment to disable the offending tests when the build
was configured with this particular flag and that solved the problem. I would
hope that this is the outcome we can achieve this time, too.

If no-one wants to make those changes for whatever reason, then that's fine and
I'll just disable the test suite in NixOS to make the build succeed. I feel like
that would be a sub-optimal solution, though.

Best regards,
Peter

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Re: [Bioc-devel] git push confusion

[Karl Stamm]

I did all that. git push upstream master says "everything up to date" and
step 7 says confirm the changes by browsing Github.
Github.org has had the changes since Friday but the build servers did not
have the changes when the build was attempted on Sunday.  Are they on a
branch other than "master"? How can I tell what the build servers are using
?

On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Please check out the documentation
>
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> > On Apr 23, 2018, at 12:13 PM, Karl Stamm  wrote:
> >
> > How do I "push to both"? I dont understand the numerous git terminology.
> On Friday I tried to push the bugfix but the build server still errors.
> > git log
> > commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master,
> upstream/master, origin/master, origin/HEAD)
> >
> > So I guess the build servers are not "upstream/master" ??
> >
> > I have this setup as given in the bioconductor documentation
> > git remote -v
> > origing...@github.com:kstammits/rgsepd.git (fetch)
> > origing...@github.com:kstammits/rgsepd.git (push)
> > upstream  g...@git.bioconductor.org:packages/rgsepd.git (fetch)
> > upstream  g...@git.bioconductor.org:packages/rgsepd.git (push)
> >
> >
> > And when I do various push commands they say "everything up to date"
> > But I want to make sure the bioc servers get the update before the 3.7
> lockdown. Is there any way to see what the are holding ?
> >
> >
> >
> >
> >
> > On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
> > Hi Karl,
> >
> > Bioconductor doesn’t automatically grab changes from your Github. A
> large body of the work is maintained only on our Bioconductor git server.
> The maintainer has to push to both Github and the Bioconductor server if
> the changes have to propagate.
> >
> > RELEASE_3_6 is now frozen forever. We announced this on April 11th. You
> cannot push to this anymore. You can still make your changes on your master
> branch.
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013212.html
> >
> > Best,
> >
> > Nitesh
> >
> >
> >
> >
> > > On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:
> > >
> > > I got a message this morning that malbec2 has build errors on my
> package.
> > > It's a bug I fixed a few days ago, but it looks like I didn't push
> changes
> > > to the right branches or something.  How do I get the bioc systems to
> take
> > > from the github updates?
> > > The help documents on the bioconductor website say to push to
> RELEASE_3_6
> > > but that doesn't seem to work. And the build server is running the
> previous
> > > code version, but calling it 3.7.
> > > I'm not sure they've gotten my changes, how can i see which versions
> the
> > > build servers have? Seems they do not automatically grab from github
> since
> > > the bug was fixed a few days ago there.
> > >
> > >   [[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.
> >
>
>
>
> 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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Re: [Bioc-devel] git push confusion

[Karl Stamm]

How do I "push to both"? I dont understand the numerous git terminology. On
Friday I tried to push the bugfix but the build server still errors.

git log

commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master,
upstream/master, origin/master, origin/HEAD)

So I guess the build servers are not "upstream/master" ??

I have this setup as given in the bioconductor documentation

git remote -v

origin g...@github.com:kstammits/rgsepd.git (fetch)

origin g...@github.com:kstammits/rgsepd.git (push)

upstream g...@git.bioconductor.org:packages/rgsepd.git (fetch)

upstream g...@git.bioconductor.org:packages/rgsepd.git (push)


And when I do various push commands they say "everything up to date"
But I want to make sure the bioc servers get the update before the 3.7
lockdown. Is there any way to see what the are holding ?





On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Karl,
>
> Bioconductor doesn’t automatically grab changes from your Github. A large
> body of the work is maintained only on our Bioconductor git server. The
> maintainer has to push to both Github and the Bioconductor server if the
> changes have to propagate.
>
> RELEASE_3_6 is now frozen forever. We announced this on April 11th. You
> cannot push to this anymore. You can still make your changes on your master
> branch.
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013212.html
>
> Best,
>
> Nitesh
>
>
>
>
> > On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:
> >
> > I got a message this morning that malbec2 has build errors on my package.
> > It's a bug I fixed a few days ago, but it looks like I didn't push
> changes
> > to the right branches or something.  How do I get the bioc systems to
> take
> > from the github updates?
> > The help documents on the bioconductor website say to push to RELEASE_3_6
> > but that doesn't seem to work. And the build server is running the
> previous
> > code version, but calling it 3.7.
> > I'm not sure they've gotten my changes, how can i see which versions the
> > build servers have? Seems they do not automatically grab from github
> since
> > the bug was fixed a few days ago there.
> >
> >   [[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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Re: [Bioc-devel] git push confusion

[Turaga, Nitesh]

Hi Karl,

Bioconductor doesn’t automatically grab changes from your Github. A large body 
of the work is maintained only on our Bioconductor git server. The maintainer 
has to push to both Github and the Bioconductor server if the changes have to 
propagate. 

RELEASE_3_6 is now frozen forever. We announced this on April 11th. You cannot 
push to this anymore. You can still make your changes on your master branch. 

https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013212.html

Best,

Nitesh 




> On Apr 23, 2018, at 11:21 AM, Karl Stamm  wrote:
> 
> I got a message this morning that malbec2 has build errors on my package.
> It's a bug I fixed a few days ago, but it looks like I didn't push changes
> to the right branches or something.  How do I get the bioc systems to take
> from the github updates?
> The help documents on the bioconductor website say to push to RELEASE_3_6
> but that doesn't seem to work. And the build server is running the previous
> code version, but calling it 3.7.
> I'm not sure they've gotten my changes, how can i see which versions the
> build servers have? Seems they do not automatically grab from github since
> the bug was fixed a few days ago there.
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] git push confusion

[Karl Stamm]

I got a message this morning that malbec2 has build errors on my package.
It's a bug I fixed a few days ago, but it looks like I didn't push changes
to the right branches or something.  How do I get the bioc systems to take
from the github updates?
The help documents on the bioconductor website say to push to RELEASE_3_6
but that doesn't seem to work. And the build server is running the previous
code version, but calling it 3.7.
I'm not sure they've gotten my changes, how can i see which versions the
build servers have? Seems they do not automatically grab from github since
the bug was fixed a few days ago there.

[[alternative HTML version deleted]]

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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Dirk Eddelbuettel]

On 23 April 2018 at 15:14, Peter Simons wrote:
| Duncan Murdoch  writes:
| 
|  > You can likely get rid of most of them by building with the recommended
|  > packages.
| 
| unfortunately, this is not an option for us. For various reasons, our
| build process requires that we build those packages separately. Ricardo
| appears to be in a similar situation and he has outlined some of those
| reasons already in his message.
| 
| Anyway, it would be FAR better for us if "make check" would simply
| succeed in the configuration we're using. We'd be perfectly happy to
| have those tests disabled that cannot be executed without the
| recommended packages available.
| 
| Is there a way to accomplish that?

I have been doing for R for about 20 years (if you count the time I assisted
Doug Bates when he was still the maintainer) (and longer for Debian), and you
seem to follow the same model we set up years ago of splitting the content of
r-recommended (itself a virtual package) off r-base-core.

You simply need to do this in stages.

As Duncan stated, this is not a concern for R Core as they offer us a way to
test the set.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Peter Simons]

Duncan Murdoch  writes:

 > You can likely get rid of most of them by building with the recommended
 > packages.

unfortunately, this is not an option for us. For various reasons, our
build process requires that we build those packages separately. Ricardo
appears to be in a similar situation and he has outlined some of those
reasons already in his message.

Anyway, it would be FAR better for us if "make check" would simply
succeed in the configuration we're using. We'd be perfectly happy to
have those tests disabled that cannot be executed without the
recommended packages available.

Is there a way to accomplish that?

Best regards,
Peter

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Re: [Bioc-devel] Warnind DaMiRseq

[Shepherd, Lori]

On quick glance this seems to indicate you are changing directories into the 
package extdata probably using a setwd -


This should not be the case -

When I look at the code, set the path to read the file to the full path 
location rather than switching into the directory that holds the data -


rawdata.path <- system.file(package = "DaMiRseq","extdata")
setwd(rawdata.path)
# import tab-delimited files:
# sample data are a small subset of Genotype-Tissue Expression (GTEx)
# RNA-Seq database (dbGap Study Accession: phs000424.v6.p1):
count_data <- read.delim("counts_import.txt")
variables_data <- read.delim("annotation_import.txt")



Don't setwd -

Instead


count_data <- read.delim(file.path(rawdata.path, "counts_import.txt"))

variables_data <- read.delim(file.path(rawdata.path, "annotation_import.txt"))


Cheers,


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 Mattia Chiesa 

Sent: Monday, April 23, 2018 3:32:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Warnind DaMiRseq

Dear All,
I am the mantainer of the DaMiRseq package. I got these Warnings in the 
Bioconductor Build/Check system but not locally:


** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting

** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting


How can I fix it?
Thanks in advance,
Mattia





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[Bioc-devel] Deadline for All Package Maintainers

[Shepherd, Lori]

This is a reminder that the last day to pass R CMD build and R CMD check is 
this Wednesday April 25th.  Please update all package that are failing on the 
build reports by this time.


Software Packages:

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

Data Experiment Packages:

http://bioconductor.org/checkResults/3.7/data-experiment-LATEST/

Workflow Packages:

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



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 
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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Ricardo Wurmus]

Hi Dirk,

> On 23 April 2018 at 12:33, Peter Simons wrote:
> | Hi,
> |
> | I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new
> | version fails its regression test suite. We configure the build using
> | the flags "--without-recommended-packages", in case that's relevant. You
> | can see a complete build log with all relevant information at [1].
> | Anyway, the test failures look like this:
>
> The flag instructs R not to build new 'recommended packages'; however the
> tests you run later need them.

Is there a way to disable only those tests that depend on the
recommended packages?  Would it make sense to disable these tests by
default when “--without-recommended-packages” is passed?

> This release has a binary change so you
> actually need to rebuild dependent packages -- in other words I think you can
> expect (some of) these tests to fail until these recommended packages are
> rebuilt.

I’ve hit the same problem as Peter in upgrading R for Guix.  We build
the recommended packages as separate packages later, so that we can
offer a minimal R package.  At the time when R itself is built the
environment does not contain any R packages, so there is nothing to be
rebuilt.

Another problem with building the recommended packages as part of the R
build process is that it’s more difficult to make them build
bit-reproducibly.  Building them as separate packages simplifies that
and enables us to prevent e.g. the embedding of timestamps.

--
Ricardo

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Re: [Bioc-devel] Process to rename a bioconductor package

[Shepherd, Lori]

We can assist we renaming -


However - we would not recommend "oma"  as that is also rather short and 
ambiguous, especially considering that is the exact abbreviated name of the 
database your package accesses -


Could you come up with perhaps a more unambigious and meaningful name?

for example here are some existing rest api for databases:

KEGGREST : Client-side REST access to KEGG

goTools:  Functions for Gene Ontology database

IMPCdata:  Retrieves data from IMPC database
InterMineR:  R Interface with InterMine-Powered Databases

BgeeDB:  Annotation and gene expression data retrieval from Bgee database


maybe something along those lines?




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 Adrian 
Altenhoff 
Sent: Thursday, April 19, 2018 4:37:07 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Process to rename a bioconductor package

Dear all,

we would like to rename or own bioconductor package 'roma' --> 'oma' (as
there exists another software tool with that name that could be
misleading). So far the package is only in the development version. Is
there a standard process how to proceed with such requests?

Thanks!
Adrian

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Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Duncan Murdoch]

On 23/04/2018 6:33 AM, Peter Simons wrote:

Hi,

I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new
version fails its regression test suite. We configure the build using
the flags "--without-recommended-packages", in case that's relevant. You
can see a complete build log with all relevant information at [1].
Anyway, the test failures look like this:


I haven't read the full script below, but a lot of it has to do with 
tests of Matrix, which is a recommended package.  Since you built 
without it, they should be expected to fail.


You can likely get rid of most of them by building with the recommended 
packages.


Duncan Murdoch



  | make[3]: Entering directory '/build/R-3.5.0/tests/Examples'
  | Testing examples for package 'base'
  | Testing examples for package 'tools'
  |   comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
  | Testing examples for package 'utils'
  | Testing examples for package 'grDevices'
  |   comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
  | Testing examples for package 'graphics'
  |   comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
  | Testing examples for package 'stats'
  |   comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE
  |   6599c6599
  |   < Grand Mean: 291.5937
  |   ---
  |   > Grand Mean: 291.5938
  |   15124c15124
  |   < Grand Mean: 291.5937
  |   ---
  |   > Grand Mean: 291.5938
  |   17444c17444
  |   < assertCondition: caught "error"
  |   ---
  |   > assertCondition: caught 'error'
  | Testing examples for package 'datasets'
  |   comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
  | Testing examples for package 'methods'
  | Testing examples for package 'grid'
  |   comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
  | Testing examples for package 'splines'
  |   comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
  | Testing examples for package 'stats4'
  |   comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
  | Testing examples for package 'tcltk'
  | Testing examples for package 'compiler'
  | Testing examples for package 'parallel'
  | make[3]: Leaving directory '/build/R-3.5.0/tests/Examples'
  | make[2]: Leaving directory '/build/R-3.5.0/tests'
  | make[2]: Entering directory '/build/R-3.5.0/tests'
  | make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make 
rule.
  | running strict specific tests
  | make[3]: Entering directory '/build/R-3.5.0/tests'
  | running code in 'eval-etc.R' ... OK
  |   comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ...414,416c414,548
  | < Warning message:
  | < In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE,  :
  | <   there is no package called 'Matrix'
  | ---
  | > Trying some Matrix objects, too
  | >
  | > Matrix> Matrix(0, 3, 2) # 3 by 2 matrix of zeros -> sparse
  | > 3 x 2 sparse Matrix of class "dgCMatrix"
  | >
  | > [1,] . .
  | > [2,] . .
  | > [3,] . .
  | >
  | > Matrix> Matrix(0, 3, 2, sparse=FALSE)# -> 'dense'
  | > 3 x 2 Matrix of class "dgeMatrix"
  | >  [,1] [,2]
  | > [1,]00
  | > [2,]00
  | > [3,]00
  | >
  | > Matrix> Matrix(0, 2, 2, sparse=FALSE)# diagonal !
  | > 2 x 2 diagonal matrix of class "ddiMatrix"
  | >  [,1] [,2]
  | > [1,]0.
  | > [2,].0
  | >
  | > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense
  | > 2 x 2 Matrix of class "dsyMatrix"
  | >  [,1] [,2]
  | > [1,]00
  | > [2,]00
  | >
  | > Matrix> Matrix(1:6, 3, 2)   # a 3 by 2 matrix (+ integer warning)
  | > 3 x 2 Matrix of class "dgeMatrix"
  | >  [,1] [,2]
  | > [1,]14
  | > [2,]25
  | > [3,]36
  | >
  | > Matrix> Matrix(1:6 + 1, nrow=3)
  | > 3 x 2 Matrix of class "dgeMatrix"
  | >  [,1] [,2]
  | > [1,]25
  | > [2,]36
  | > [3,]47
  | >
  | > Matrix> ## logical ones:
  | > Matrix> Matrix(diag(4) >  0)# -> "ldiMatrix" with diag = "U"
  | > 4 x 4 diagonal matrix of class "ldiMatrix"
  | >  [,1] [,2] [,3] [,4]
  | > [1,] TRUE...
  | > [2,]. TRUE..
  | > [3,].. TRUE.
  | > [4,]... TRUE
  | >
  | > Matrix> Matrix(diag(4) >  0, sparse=TRUE)# -> sparse...
  | > 4 x 4 sparse Matrix of class "lsCMatrix"
  | >
  | > [1,] | . . .
  | > [2,] . | . .
  | > [3,] . . | .
  | > [4,] . . . |
  | >
  | > Matrix> Matrix(diag(4) >= 0)# -> "lsyMatrix" (of all 'TRUE')
  | > 4 x 4 Matrix of class "lsyMatrix"
  | >  [,1] [,2] [,3] [,4]
  | > [1,] TRUE TRUE TRUE TRUE
  | > [2,] TRUE TRUE TRUE TRUE
  | > [3,] TRUE TRUE TRUE TRUE
  | > [4,] TRUE TRUE TRUE TRUE
  | >
  | > Matrix> ## triangular
  | > Matrix> l3 <- upper.tri(matrix(,3,3))
  | >
  | > Matrix> (M <- Matrix(l3))  # -> "ltCMatrix"
  | > 3 x 3 sparse Matrix of class "ltCMatrix"
  | >
  | > [1,] . | |
  | > [2,] . . |
  | > [3,] . . .
  | >
  | > Matrix> Matrix(! l3)# -> "ltrMatrix"
  | > 3 x 3 Matrix of class "ltrMatrix"
  | 

Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Dirk Eddelbuettel]

On 23 April 2018 at 12:33, Peter Simons wrote:
| Hi,
| 
| I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new
| version fails its regression test suite. We configure the build using
| the flags "--without-recommended-packages", in case that's relevant. You
| can see a complete build log with all relevant information at [1].
| Anyway, the test failures look like this:

The flag instructs R not to build new 'recommended packages'; however the
tests you run later need them.  This release has a binary change so you
actually need to rebuild dependent packages -- in other words I think you can
expect (some of) these tests to fail until these recommended packages are
rebuilt.

>From the doc/NEWS file, lines 395 and on:

* The object header layout has been changed to support merging the
  ALTREP branch. This requires re-installing packages that use
  compiled code.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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[Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

[Peter Simons]

Hi,

I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new
version fails its regression test suite. We configure the build using
the flags "--without-recommended-packages", in case that's relevant. You
can see a complete build log with all relevant information at [1].
Anyway, the test failures look like this:

 | make[3]: Entering directory '/build/R-3.5.0/tests/Examples'
 | Testing examples for package 'base'
 | Testing examples for package 'tools'
 |   comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
 | Testing examples for package 'utils'
 | Testing examples for package 'grDevices'
 |   comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
 | Testing examples for package 'graphics'
 |   comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
 | Testing examples for package 'stats'
 |   comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE
 |   6599c6599
 |   < Grand Mean: 291.5937
 |   ---
 |   > Grand Mean: 291.5938
 |   15124c15124
 |   < Grand Mean: 291.5937
 |   ---
 |   > Grand Mean: 291.5938
 |   17444c17444
 |   < assertCondition: caught "error"
 |   ---
 |   > assertCondition: caught 'error'
 | Testing examples for package 'datasets'
 |   comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
 | Testing examples for package 'methods'
 | Testing examples for package 'grid'
 |   comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
 | Testing examples for package 'splines'
 |   comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
 | Testing examples for package 'stats4'
 |   comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
 | Testing examples for package 'tcltk'
 | Testing examples for package 'compiler'
 | Testing examples for package 'parallel'
 | make[3]: Leaving directory '/build/R-3.5.0/tests/Examples'
 | make[2]: Leaving directory '/build/R-3.5.0/tests'
 | make[2]: Entering directory '/build/R-3.5.0/tests'
 | make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make 
rule.
 | running strict specific tests
 | make[3]: Entering directory '/build/R-3.5.0/tests'
 | running code in 'eval-etc.R' ... OK
 |   comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ...414,416c414,548
 | < Warning message:
 | < In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE,  :
 | <   there is no package called 'Matrix'
 | ---
 | > Trying some Matrix objects, too
 | >
 | > Matrix> Matrix(0, 3, 2) # 3 by 2 matrix of zeros -> sparse
 | > 3 x 2 sparse Matrix of class "dgCMatrix"
 | >
 | > [1,] . .
 | > [2,] . .
 | > [3,] . .
 | >
 | > Matrix> Matrix(0, 3, 2, sparse=FALSE)# -> 'dense'
 | > 3 x 2 Matrix of class "dgeMatrix"
 | >  [,1] [,2]
 | > [1,]00
 | > [2,]00
 | > [3,]00
 | >
 | > Matrix> Matrix(0, 2, 2, sparse=FALSE)# diagonal !
 | > 2 x 2 diagonal matrix of class "ddiMatrix"
 | >  [,1] [,2]
 | > [1,]0.
 | > [2,].0
 | >
 | > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense
 | > 2 x 2 Matrix of class "dsyMatrix"
 | >  [,1] [,2]
 | > [1,]00
 | > [2,]00
 | >
 | > Matrix> Matrix(1:6, 3, 2)   # a 3 by 2 matrix (+ integer warning)
 | > 3 x 2 Matrix of class "dgeMatrix"
 | >  [,1] [,2]
 | > [1,]14
 | > [2,]25
 | > [3,]36
 | >
 | > Matrix> Matrix(1:6 + 1, nrow=3)
 | > 3 x 2 Matrix of class "dgeMatrix"
 | >  [,1] [,2]
 | > [1,]25
 | > [2,]36
 | > [3,]47
 | >
 | > Matrix> ## logical ones:
 | > Matrix> Matrix(diag(4) >  0)# -> "ldiMatrix" with diag = "U"
 | > 4 x 4 diagonal matrix of class "ldiMatrix"
 | >  [,1] [,2] [,3] [,4]
 | > [1,] TRUE...
 | > [2,]. TRUE..
 | > [3,].. TRUE.
 | > [4,]... TRUE
 | >
 | > Matrix> Matrix(diag(4) >  0, sparse=TRUE)# -> sparse...
 | > 4 x 4 sparse Matrix of class "lsCMatrix"
 | >
 | > [1,] | . . .
 | > [2,] . | . .
 | > [3,] . . | .
 | > [4,] . . . |
 | >
 | > Matrix> Matrix(diag(4) >= 0)# -> "lsyMatrix" (of all 'TRUE')
 | > 4 x 4 Matrix of class "lsyMatrix"
 | >  [,1] [,2] [,3] [,4]
 | > [1,] TRUE TRUE TRUE TRUE
 | > [2,] TRUE TRUE TRUE TRUE
 | > [3,] TRUE TRUE TRUE TRUE
 | > [4,] TRUE TRUE TRUE TRUE
 | >
 | > Matrix> ## triangular
 | > Matrix> l3 <- upper.tri(matrix(,3,3))
 | >
 | > Matrix> (M <- Matrix(l3))  # -> "ltCMatrix"
 | > 3 x 3 sparse Matrix of class "ltCMatrix"
 | >
 | > [1,] . | |
 | > [2,] . . |
 | > [3,] . . .
 | >
 | > Matrix> Matrix(! l3)# -> "ltrMatrix"
 | > 3 x 3 Matrix of class "ltrMatrix"
 | >  [,1]  [,2]  [,3]
 | > [1,]  TRUE . .
 | > [2,]  TRUE  TRUE .
 | > [3,]  TRUE  TRUE  TRUE
 | >
 | > Matrix> as(l3, "CsparseMatrix")
 | > 3 x 3 sparse Matrix of class "lgCMatrix"
 | >
 | > [1,] . | |
 | > [2,] . . |
 | > [3,] . . .
 | >
 | > Matrix> Matrix(1:9, nrow=3,
 | > Matrix+dimnames = list(c("a", "b", "c"), c("A", "B", "C")))
 | > 3 x 3 Matrix of class "dgeMatrix"
 | >   A B C
 | > a 1 4 7
 | > b 2 5 8
 | > c 3 6 9
 | >
 | 

Re: [Bioc-devel] Transition from Google Sheet to Web App

[Obenchain, Valerie]

Hi Ashish Jain,

The email you registered with the Google Sheet was 
'ge...@iastate.edu'.

The email in the DESCRIPTION file often goes stale. If a maintainer registered 
with the Google Sheet with an address different from DESCRIPTION we performed 
several checks. If the username provided in the Google Sheet matched the config 
and keys we have on file, it was assumed the email in the Google Sheet was more 
current.

Is ge...@iastate.edu an email for you or no?

Valerie


On 04/20/2018 01:02 PM, Ashish Jain wrote:
Hi,

I am the developer of the "TissueEnrich" package and I tried to activate my 
account using my email id in DESCRIPTION file 
(j...@iastate.edu) but the site is saying 
"j...@iastate.edu is not associated with a maintainer 
of a Bioconductor package". Can you please help me with this.

Regards,
Ashish Jain

On Wed, Apr 18, 2018 at 1:05 PM, Turaga, Nitesh 
> wrote:
The Web App for managing SSH keys is now available at

  https://git.bioconductor.org/BiocCredentials/

Accounts have been created for all package maintainers. Note the central 
identifier, i.e., how you login is your email. This email was taken from the 
DESCRIPTION of your package or the Google Sheet if you registered a key there.

When you first visit the App you'll need to activate your account. An 
activation link will be sent to your email. Once your account is activated you 
can login. Trying to login without activation will lead to an error.

Let us know if you have any questions or problems.

Best Regards,



> On Apr 18, 2018, at 8:56 AM, Obenchain, Valerie 
>  wrote:
>
> This transition will start at 9am EST today. We'll post back when it's done.
>
> Valerie
>
>
> On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:
>
> Hi developers,
>
> Tomorrow we are bringing a web app online to help with the management of SSH 
> keys. The app will replace the Google Sheet currently used to add keys. 
> Through the web interface you'll be able to add keys and change your email or 
> github username. There is also an option to see what packages you have access 
> to.
>
> Using the app is not a requirement. It's intended to help package authors get 
> setup with keys and access to their package in the Bioconductor git 
> repository. Those of you already set up with keys and access may never need 
> to use it.
>
> Tomorrow, April 18, we'll have downtime from 9-11am EST while we take down 
> the Google Sheet and bring up the app.
>
> Thanks.
>
> Valerie and Nitesh
>
>
> 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.
>[[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.
>   [[alternative HTML version deleted]]
>
> ___
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This email message may contain legally privileged and/or confidential 
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--
Regards,
Ashish Jain
BCB-Graduate Student
Iowa State University
Ph +1-317-529-7973
Website: 

Re: [Bioc-devel] Transition from Google Sheet to Web App

[Ashish Jain]

Hi Valerie,

Thank you for this information. It is the email of my PI. I will tell her
to register on this website. Again thank you for the information.

Regards,
Ashish Jain

On Fri, Apr 20, 2018 at 3:26 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Ashish Jain,
>
> The email you registered with the Google Sheet was 'ge...@iastate.edu'.
>
> The email in the DESCRIPTION file often goes stale. If a maintainer
> registered with the Google Sheet with an address different from DESCRIPTION
> we performed several checks. If the username provided in the Google Sheet
> matched the config and keys we have on file, it was assumed the email in
> the Google Sheet was more current.
>
> Is ge...@iastate.edu an email for you or no?
>
> Valerie
>
>
>
> On 04/20/2018 01:02 PM, Ashish Jain wrote:
>
> Hi,
>
> I am the developer of the "TissueEnrich" package and I tried to activate
> my account using my email id in DESCRIPTION file (j...@iastate.edu) but
> the site is saying "j...@iastate.edu is not associated with a maintainer
> of a Bioconductor package". Can you please help me with this.
>
> Regards,
> Ashish Jain
>
> On Wed, Apr 18, 2018 at 1:05 PM, Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> The Web App for managing SSH keys is now available at
>>
>>   https://git.bioconductor.org/BiocCredentials/
>>
>> Accounts have been created for all package maintainers. Note the central
>> identifier, i.e., how you login is your email. This email was taken from
>> the DESCRIPTION of your package or the Google Sheet if you registered a key
>> there.
>>
>> When you first visit the App you'll need to activate your account. An
>> activation link will be sent to your email. Once your account is activated
>> you can login. Trying to login without activation will lead to an error.
>>
>> Let us know if you have any questions or problems.
>>
>> Best Regards,
>>
>>
>>
>> > On Apr 18, 2018, at 8:56 AM, Obenchain, Valerie
>>  wrote:
>> >
>> > This transition will start at 9am EST today. We'll post back when it's
>> done.
>> >
>> > Valerie
>> >
>> >
>> > On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:
>> >
>> > Hi developers,
>> >
>> > Tomorrow we are bringing a web app online to help with the management
>> of SSH keys. The app will replace the Google Sheet currently used to add
>> keys. Through the web interface you'll be able to add keys and change your
>> email or github username. There is also an option to see what packages you
>> have access to.
>> >
>> > Using the app is not a requirement. It's intended to help package
>> authors get setup with keys and access to their package in the Bioconductor
>> git repository. Those of you already set up with keys and access may never
>> need to use it.
>> >
>> > Tomorrow, April 18, we'll have downtime from 9-11am EST while we take
>> down the Google Sheet and bring up the app.
>> >
>> > Thanks.
>> >
>> > Valerie and Nitesh
>> >
>> >
>> > 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.
>> >[[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.
>> >   [[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.
>> 

Re: [Bioc-devel] Transition from Google Sheet to Web App

[Ashish Jain]

Hi,

I am the developer of the "TissueEnrich" package and I tried to activate my
account using my email id in DESCRIPTION file (j...@iastate.edu) but
the site is saying "j...@iastate.edu is not associated with a maintainer of
a Bioconductor package". Can you please help me with this.

Regards,
Ashish Jain

On Wed, Apr 18, 2018 at 1:05 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> The Web App for managing SSH keys is now available at
>
>   https://git.bioconductor.org/BiocCredentials/
>
> Accounts have been created for all package maintainers. Note the central
> identifier, i.e., how you login is your email. This email was taken from
> the DESCRIPTION of your package or the Google Sheet if you registered a key
> there.
>
> When you first visit the App you'll need to activate your account. An
> activation link will be sent to your email. Once your account is activated
> you can login. Trying to login without activation will lead to an error.
>
> Let us know if you have any questions or problems.
>
> Best Regards,
>
>
>
> > On Apr 18, 2018, at 8:56 AM, Obenchain, Valerie 
> > 
> wrote:
> >
> > This transition will start at 9am EST today. We'll post back when it's
> done.
> >
> > Valerie
> >
> >
> > On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:
> >
> > Hi developers,
> >
> > Tomorrow we are bringing a web app online to help with the management of
> SSH keys. The app will replace the Google Sheet currently used to add keys.
> Through the web interface you'll be able to add keys and change your email
> or github username. There is also an option to see what packages you have
> access to.
> >
> > Using the app is not a requirement. It's intended to help package
> authors get setup with keys and access to their package in the Bioconductor
> git repository. Those of you already set up with keys and access may never
> need to use it.
> >
> > Tomorrow, April 18, we'll have downtime from 9-11am EST while we take
> down the Google Sheet and bring up the app.
> >
> > Thanks.
> >
> > Valerie and Nitesh
> >
> >
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> >
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> >
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-- 
Regards,
Ashish Jain
BCB-Graduate Student
Iowa State University
Ph +1-317-529-7973
Website: *https://ashishjain1988.github.io/
*
Github: https://github.com/ashishjain1988/

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[Bioc-devel] Warnind DaMiRseq

[Mattia Chiesa]

Dear All,
I am the mantainer of the DaMiRseq package. I got these Warnings in the 
Bioconductor Build/Check system but not locally:


** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting

** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting


How can I fix it?
Thanks in advance,
Mattia





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