Hi,
I was playing around with inotifywait (great tool!) to see the new
staged installation of source packages in action. In one terminal I'm
monitoring the create/delete/move events of the installation library with:
inotifywait -m --timefmt '%F %T' --format '%T -- %w %e %f' -e create
-e
Yes I strongly second Robert's suggestion.
Also be sure that you are registered at https://support.bioconductor.org and
that you enter your package name in the 'Watched tags' field of the user
Profile, so that you are notified by email whenever a question is posted there.
Martin
On 4/24/19,
Hi Stian,
This is likely related to an issue with the recently updated
org.Hs.eg.db package. The issue was reported on this list 2 days ago:
https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014956.html
A fix for org.Hs.eg.db is on its way. Hopefully it will make the current
test failure
Instead of putting the message in the startup, perhaps make use of
the BugReports field in the package DESCRIPTION, and maybe use a GitHub
issues page with a good template
This way you avoid annoying your users with startup messages, for something
that should be accessible in the DESCRIPTION
Hi,
The most recent build of chimeraviz failed due to a test failure:
https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/chimeraviz/malbec2-checksrc.html.
That the test in question should suddenly fail surprises me, and I'm unable
to reproduce this locally. Does anyone have ideas as to
On 4/24/19 10:48, Pages, Herve wrote:
> Hi developers,
>
> Due to some technical problems with the build system, there will be no
> new build report today for the BioC 3.10 software builds.
I meant for the BioC 3.9 builds sorry.
(There won't be a report for the BioC 3.10 builds either but these
Thank you very much for your kind help. That fixed my issue.
Best regards,
Arman
From: Shepherd, Lori
Sent: Wednesday, April 24, 2019 9:59:40 PM
To: Arman Shahrisa; Martin Morgan; bioc-devel; szwj...@gmail.com
Subject: Re: [Bioc-devel] How can I print a message
Hi developers,
Due to some technical problems with the build system, there will be no
new build report today for the BioC 3.10 software builds.
Sorry for the inconvenience.
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research
I assume your package is the cbaf package?
Don't forget the new zzz.R file to the collate field in the DESCRIPTION
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
I really appreciate your kind answers. I created the zzz.R file in the same
folder as the rest
of my R files. I tried both .onAttach and .onLoad functions as follow:
> .onAttach <- function(libname, pkgname){
>packageStartupMessage("Please send bug reports and suggestions to
>
Hi Astrid
Your package should be good to go now as far as the "master" (devel) branch
goes. Don't worry about the RELEASE_3_8 having duplicate commit issues, it
doesn't need to be fixed since it's been frozen (i.e you cannot issue changes
to it anymore).
But from the upcoming release, please
Yep, I know. Well, maybe I didn't, but there are also issues with propagation
of fixedness in constrained optimization.
Revising mle() had neen on my todo list for way too long. The bbmle package
handles this better, I believe.
-pd
> On 24 Apr 2019, at 16:51 , Stefano de Pretis wrote:
>
>
Dear R developers,
I noticed a bug in the stats4 package, specifically in the confint method
applied to “mle” objects.
In particular, when some “fixed” parameters define the log likelihood, these
parameters are stored within the mle object but they are not used by the
“confint" method, which
--- Begin Message ---
HI:
Though you appear to have found the problem. it is a package called plotdap,
the Ubuntu results are here:
https://builder.r-hub.io/status/plotdap_0.0.1.tar.gz-5e8cf0d2b8304290820438dde5593e27
The complete build attempt was:
> #> * installing *source* package
OK, so I did the archaeology anyway
This was the story, R-core November 29, 2001. Part of thread "X11 still
segfaults".
>>
.
Gah. I've been too tired today. Why did that take me so long?
The culprit seems to be
R_ProcessEvents((void*) NULL)
in newX11DeviceDriver
This
On 4/18/19 11:07 PM, Jack Wasey wrote:
I was trying to get an interactive R prompt with the current working directory.
I reviewed R source 'main.c' and 'options.c', and saw that a 20 char buffer is
used when in Browse debugging mode, but that no other validation is done on the
length of the
Incorrect code,
A <- matrix(1, 2, 2)
B <- matrix(2, 3, 2)
A %*% B
Produces
Error in A %*% B : non-conformable arguments
It would be helpful to show the matrix dimensions,
Error in A %*% B : non-conformable arguments of dimensions (2, 2) and (3, 2)
--
Joshua N. Pritikin, Ph.D.
Virginia
I appreciate the writing on this.
However I definitely think there is a huge difference between "use with care"
and "don't use". They just are not the same statement.
> On Mar 29, 2019, at 10:15 AM, Simon Urbanek
> wrote:
>
> Jim,
>
> I think the main point of Tomas' post was to alert R
Hi,
there can be an issue with recent gcc where the system-installed "ar"
and "ranlib" commands cannot handle LTO binaries. On compilation, this
manifests itself with error messages claiming that they need extra
plugins.
This can be fixed by using the command line
$ AR=gcc-ar
Seems like GDAL is too old on our Ubuntu:
https://github.com/r-hub/rhub/issues/258
Will try to fix soon.
FYI,
G.
On Wed, Apr 24, 2019 at 10:08 AM Gábor Csárdi wrote:
>
> Hi, which package is this, and how exactly did rgdal fail?
>
> Also, you can report R-hub problems at
I don't recall exactly what I did 18 years ago eiher and I likely don't have
the time to dig into the archives and reconstruct.
I can imagine that the issue had to do with the protocol around creating and
mapping windows. Presumably the segfault comes from looking for events on a
window that
Hi, which package is this, and how exactly did rgdal fail?
Also, you can report R-hub problems at https://github.com/r-hub/rhub/issues
Thanks,
Gabor
On Wed, Apr 24, 2019 at 1:11 AM Roy Mendelssohn - NOAA Federal via
R-package-devel wrote:
>
>
>
>
> -- Forwarded message --
>
On 24.04.2019 11:08, Berry Boessenkool wrote:
Hi,
I have a package with some keyboard shortcuts for Rstudio. Several friends and
colleagues asked me to put it on CRAN.
It includes a function to set the keyboard bindings that will write to
~/.R/rstudio/keybindings/addins.json et al.
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