Hi all,
We have a package that is currently under review for inclusion, and on the
release schedule page [1] the deadline for package submissions is today.
Does this mean that packages that are currently under review are not going to
be included in the 3.4 release?
Kind regards,
Roel Janssen
On Monday, September 26, 2016 12:46 PM, Martin Morgan wrote:
> On 09/26/2016 06:13 AM, Janssen-10, R.R.E. wrote:
>> Hi all,
>>
>> We have a package that is currently under review for inclusion, and
>> on the release schedule page [1] the deadline for package submissi
Dear list,
The automated building of our package on Windows seems to yield a warning I
don't think I can resolve (see [1]).
The relevant error is:
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'digest'
Error: package 'pkgmaker' could n
Hello all,
We wrote our vignette in Sweave/LaTeX, and I am running into a problem with
citing to other papers.
I would like to use the APA style of citing which looks like: "Determine the
optimal factorization rank using the NMF package (Gaujoux and Seoighe, 2010).
..."
Now, to achieve that, I
Obenchain, Valerie writes:
> Hi,
>
> On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote:
>> Hello all,
>>
>> We wrote our vignette in Sweave/LaTeX, and I am running into a problem with
>> citing to other papers.
>> I would like to use the APA style of
Dear Valerie,
We're working on MutationalPatterns as you can see (we've had our last changes
pushed into the SVN repository just two days ago).
Due to the timezone differences between Europe and the US, we seem to be
missing out the starting point of a new build round.
So, at which time do you
Dear Bioconductor team,
It seems that the download links for the package source of 'DelayedArray' are
missing. See:
https://bioconductor.org/packages/3.5/bioc/html/DelayedArray.html
The link:
https://bioconductor.org/packages/3.5/bioc/src/contrib/DelayedArray_0.1.11.tar.gz
Seems broken.
Kind r
Dear Bioconductor developers,
What's the proper way of applying bugfixes to both the 3.5 release branch and
the devel branch?
Should I simply commit the same things twice?
Kind regards,
Roel Janssen
--
De informatie op
Dear Bioconductorians,
Is there something wrong with malbec2, or is there something broken in our
package?
See the build report:
http://bioconductor.org/checkResults/release/bioc-LATEST/MutationalPatterns/malbec2-buildsrc.html
Kind regards,
Roel Janssen
this and a fix will be coming soon.
>
> Valerie
> On 05/10/2017 02:23 AM, Janssen-10, R.R.E. wrote:
>> Dear Bioconductorians,
>>
>> Is there something wrong with malbec2, or is there something broken in our
>> package?
>>
>> See the build report:
From: Obenchain, Valerie [valerie.obench...@roswellpark.org]
>
> Hi Roel,
>
> Looks like the problem is in rtracklayer (also red on the release build
> report). I think Michael is aware of this and a fix will be coming soon.
>
> Valerie
> On 05/10/2017 02:23 AM, Janssen-1
Dear Valerie,
Could we maybe do a manual build for the package, so that the bugfixed version
can be propagated to users?
Kind regards,
Roel Janssen
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Janssen-10,
R.R.E. [r.r.e.janssen
Hello,
It seems that the tarball BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz has changed,
without a change in version:
>From
>http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz...
...SC.hg19_1.4.0.tar.gz 656.3MiB 5.6MiB/s 01:58 [###
: Sunday, July 23, 2017 7:44 PM
To: Vincent Carey; Janssen-10, R.R.E.
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Change in BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz
Hi,
BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz was added to Bioconductor
in BioC 3.0 and has not changed since then. At least
Hello Hervé,
> Hi,
>
> On 07/30/2017 03:28 AM, Janssen-10, R.R.E. wrote:
>> Hello,
>>
>> So, are you absolutely sure nothing has changed in this package?
>
> All I'm saying it that version 1.4.0 of this package has not changed
> since it was first made
Dear Bioconductor team,
I cannot push to the master branch of our package (MutationalPatterns).
$ git push origin master
fatal: remote error: FATAL: W any packages/MutationalPatterns nobody DENIED by
fallthru
(or you mis-spelled the reponame)
$ git remote -v
origin https://git.bioconductor.org
Dear Bioconductor maintainers,
The build report for our package 'MutationalPatterns' signals a warning for
functions that are deprecated. I explicitly added "@noRd" to the function
header to prevent it from ending up in the documentation. How should I go
about fixing this warning?
The other
Dear,
It seems that the 3.6 release contains an old version of the vignette of
MutationalPatterns.
In commit d1c4e14 I pushed updates of the corresponding bioRxiv paper, but the
changes in the vignette haven't made it in.
Should I now bump the release number without making any further changes?
Dear Bioconductor,
The build for MutationalPatterns has been failing for a week. The exact same
code built fine, because the last commit ups the version number to 1.4.1, which
is the version that is available on Bioconductor.
I also cannot reproduce the error with the code from upstream on my
Hi Martin,
Thanks for your reply!
Martin Morgan writes:
> On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote:
>> Dear Bioconductor,
>>
>> The build for MutationalPatterns has been failing for a week. The exact
>> same code built fine, because the last commit ups the
Dear Martin,
Martin writes:
> On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote:
>> Hi Martin,
>>
>> Thanks for your reply!
>>
>> Martin Morgan writes:
>>
>>> On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote:
>>>> Dear Bioconductor,
>
Dear all,
Users of our package report an error every now and then when running NMF [1].
The error looks like this:
Error: NMF::nmf - 100/100 fit(s) threw an error.
# Error(s) thrown:
- run #1: unused arguments (model = list(model = "NMFstd", rank = 5, target =
0), method = "random")
Which is
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