Let's see what Henrik says, he is a Windows user. I'll look at getting a VM.
Kasper
On Thu, Mar 31, 2016 at 9:31 PM, Dan Tenenbaum
wrote:
> I asked Jim Hester about affxparser and he said:
>
> > affxparser - Looks like they are overriding the WINVAR constant (
> >
> https://github.com/Bioconduc
I asked Jim Hester about affxparser and he said:
> affxparser - Looks like they are overriding the WINVAR constant (
> https://github.com/Bioconductor-mirror/affxparser/blob/master/src/R_affx_constants.h#L17),
> which is causing the windows symbols to be missed. You may want to try
> commenting th
There are tons of errors with affxparser (as mentioned on the toolchain
setup documentation). However, (almost) all of them seems to be errors in
header files included with mingq. The first one is pasted below, and the
error (seems to be) in the minwindef.h header file. Given that this is a
new
Hi,
I repeated several times the clone And I success for one time the
commit but with mistakes. I can't repeat the steps again.
git merge master --log
And I had a conflict between versions. I omit conflicts and I
git svn dcommit --add-author-from
##
A
A.
I can also run the example on i386. Seems to just affect x64; let me know if
your experience is different when you try this on a 64-bit machine.
I'll add this data point to the issue.
Dan
- Original Message -
> From: "Ramon Diaz-Uriarte"
> To: "Dan Tenenbaum"
> Cc: "Luca De Sano" ,
Hi Dan,
OncoSimulR is also afflicted by this
(https://www.bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/moscato2-buildsrc.html).
However,
like Luca, I cannot reproduce the issue: I followed your instructions, and I
was able to build (and check) the package without problem.
Moreover,
I agree. The importExcept idea also works that way: importExcept(foo, bar, baz)
But import(foo, except=c(bar, baz)) reads better.
On Thu, Mar 31, 2016 at 4:00 PM, wrote:
> I don't think you want to separate it from the import. Better to allow
> something like
>
> import(foo, exclude=bar)
>
> o
I don't think you want to separate it from the import. Better to allow
something like
import(foo, exclude=bar)
or
import(foo, exclude=c("bar", "baz"))
This seems reasonably natural and shouldn't be too hard to
implement. (But is has been a while since I've worked on this code).
Best,
luke
O
I think "From" is needed to specify which package we want to exlude
functions.
I think excludeFrom (package, function) seems to be intuitive.
thanks,
Karim
On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès wrote:
> On 03/31/2016 12:55 PM, Michael Lawrence wrote:
>
>> Probably should just stick
On 03/31/2016 12:55 PM, Michael Lawrence wrote:
Probably should just stick to exact symbols for now. If there is a
case where a pattern is actually useful, rather than just an
obfuscation, we can extend the feature set.
Fair enough. Not really intuitive that excludeImport uses the same
syntax a
I think it's a problem with igraph (a CRAN package) under the new toolchain. I
was just in the process of filing a github issue with that package maintainer.
Watch for it at https://github.com/igraph/igraph/issues/ .
Dan
- Original Message -
> From: "Luca De Sano"
> To: "bioc-devel"
Hi all,
the build of our package TRONCO fails with this error on the Windows test
machine:
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
"R_igraph_make_weak_ref" not available for .Call() for package "igraph"
Execution halted
as reported in
http://bioconductor.org/checkResult
Probably should just stick to exact symbols for now. If there is a
case where a pattern is actually useful, rather than just an
obfuscation, we can extend the feature set.
On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie)
wrote:
> Herve,
>
> That is a very interesting idea and works for me! Th
Herve,
That is a very interesting idea and works for me! Thanks!
importPatternFrom(IRanges, "^values$")
Best,
Julie
On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé Pagès"
wrote:
>On 03/30/2016 08:35 PM, Michael Lawrence wrote:
>> That would work, but R is not going to be happy about redu
Hi,
We have made a temporary change to the schedule of the builds.
Experiment Data packages will now build just once a week, on Saturdays during
the day (Seattle time).
Software packages will build every day of the week EXCEPT Friday night/Saturday
morning.
At the moment we're stuck with limi
On 03/30/2016 08:35 PM, Michael Lawrence wrote:
That would work, but R is not going to be happy about redundant
imports. Interactively, users would balk at symbol qualification.
There are two classes of conflict:
1) Same semantics, where a common generic would arbitrate, or one
package could dep
You might also consider whether you really need the hash package. It
seems like a pretty lightweight wrapper around environments.
On Thu, Mar 31, 2016 at 7:16 AM, Zhu, Lihua (Julie)
wrote:
> Thanks Kasper! Importing Iranges piecewise is difficult.
>
> Michael, I did use importFrom(hash, …)
>
> im
Hi Hamada,
Bioconductor has two branches - release and development. ExperimentHub
has been added to the devel branch of Bioconductor recently -and it
will thus work only with the devel version of R until it is added to the
release branch ( April 15th, 2016)
The release schedule can be found he
On 03/31/2016 07:05 AM, Michael Lawrence wrote:
We should probably deprecate values(). It has long been superseded by
mcols().
FWIW this is on my long-term list but it can't be done now. values()
was originally (and is still) a RangedData accessor. At some point it
was also made a synonym of el
Hello all,
R is planning to use a new Windows toolchain (known as Rtools33) for the
soon-to-be-released R-3.3.0.
This toolchain will use gcc/g++ 4.9.3 (an upgrade from 4.6.3).
We expect CRAN packages for Windows using this toolchain in a few days.
We are currently building the devel branch of B
You have two titles in the vignette and the second one is blank:
dtenenba@Dans-Air:~/devel/CINdex/vignettes$ grep VignetteIndexEntry CINdex.Rnw
%\VignetteIndexEntry{CINTutorial}
%\VignetteIndexEntry{}
Remove the second one.
Dan
- Original Message -
> From: "Krithika Bhuvaneshwar"
> To
Hello,
We are working on fine tuning our newly pre-accepted BioC package.
We have two vignettes - an .Rnw file and another .Rmd file.
If you see the screen shot in this email, you will see that there is
no title or tag for my .Rnw file seen (first document in screen shot).
But the .Rmd file vign
There were no windows build results yesterday, and Snow Leopard builds stopped
some time ago. So nothing needs to be done.
Dan
- Original Message -
> From: "Maarten van Iterson"
> To: "bioc-devel"
> Sent: Thursday, March 31, 2016 12:01:04 AM
> Subject: [Bioc-devel] not yet updated pack
R is not going to be able to support all possible qualifications of
authorship. If they are authors (i.e., they should be cited), then
list them as "aut" and either rely on people's assumptions about the
order of the authors and/or document the specific contributions in the
package-level man page.
Hello,
We are working on fine tuning how the citation should look in our
DESCRIPTION of our pre-accepted package.
We would like our R citation to appear like this:
Author1, Author2, Author3, Author4, Author5, Author6 and Author7
(2016), PackageName. R package version 0.99.9.
Just like how we wr
But using hash::values() is not so bad.
On Thu, Mar 31, 2016 at 7:09 AM, Kasper Daniel Hansen
wrote:
> Of course, that depends on whether Julie actually uses hash::values or this
> is just trying to avoid a conflict. Importing IRanges piecewise is ...
> probably difficult.
>
> Best,
> Kasper
>
>
Thanks Kasper! Importing Iranges piecewise is difficult.
Michael, I did use importFrom(hash, …)
importFrom(hash, values, hash)
Also, this is just an example. Thanks for willing to add a function similar to
importFromExcept()
Best,
Julie
From: Kasper Daniel Hansen
mailto:kasperdanielhan...@
Of course, that depends on whether Julie actually uses hash::values or this
is just trying to avoid a conflict. Importing IRanges piecewise is ...
probably difficult.
Best,
Kasper
On Thu, Mar 31, 2016 at 10:05 AM, Michael Lawrence <
lawrence.mich...@gene.com> wrote:
> We should probably depreca
We should probably deprecate values(). It has long been superseded by
mcols(). But for now, it would seem pragmatic to importFrom(hash, ...)
since it has so few functions.
On Thu, Mar 31, 2016 at 6:54 AM, Zhu, Lihua (Julie)
wrote:
> Sorry. I meant values.
>
> replacing previous import ŒIRanges::v
Sorry. I meant values.
replacing previous import ŒIRanges::values¹ by Œhash::values¹ when loading
ŒCRISPRseek¹
Best,
Julie
On 3/30/16 11:13 PM, "Michael Lawrence" wrote:
>I can't find the hash function in IRanges. Are you sure it has one?
>
>On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Juli
Dear all,
Should I worry about not yet updated package sources/binaries in devel:
Package Source MethylAid_1.5.3.tar.gz
Windows Binary None
Mac OS X 10.6 (Snow Leopard) MethylAid_1.3.1.tgz
Mac OS X 10.9 (Mavericks) MethylAid_1.5.3.tgz
For example, no binary for windows and old so
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