On 03/29/2017 12:57 AM, Dan Tenenbaum wrote:
Don't install R-3.5; install R-3.4 from
https://cran.rstudio.com/bin/windows/base/rtest.html
Expanding a little --
R has a yearly release cycle, Bioc a 6 month release cycle
Bioc-devel tries to use the R that will be used when Bioc-devel becomes
Hi,
our package epiNEM produces an error on the linux builder, due to some missing
pcalg library. This seems to be an error on the builder’s end, because the
packages ddgraph and miRLAB suffer the same error, also exclusively for the
linux builder. Does that problem go hand in hand with the fac
I am developing a web application using Shiny to be distributed as
Bioconductor package. I would like to know if there are some
recommendations for better integration with Bioconductor ecosystem.
Best regards,
Welliton
[[alternative HTML version deleted]]
Hi Wellinton,
As far as I know if you wrap you shiny stuff into an R function that should
be enough. Then you can provide both non-interactive and interactive
functions and the user can choose what to run.
You can have a look at my SC3 package where I implemented a strategy above:
https://github.
Hi all,
I receive this error when loading rtracklayer in my vignette which is
stopping my package from building:
Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 39-50 (heatmaps.Rmd)
Error: processing vignette 'heatmaps.Rmd' failed with diagnostics:
pac
It looks like things got out of sync with some recent shuffling. A
change to Biostrings made it through to the latest builds, but not the
change to rtracklayer. There should be a fixed version of rtracklayer
available soon, or you could grab it from svn.
On Wed, Mar 29, 2017 at 7:49 AM, Malcolm Pe
Hi,
I got the error “object ‘inverted’ is not exported by 'namespace:Biostrings” at
http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due to
the package “Biostrings” which failed to pass the check
(http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it
r
Hi:
This happened to me several times, and I figured out the issue. I tried to
remove `rtracklayer` package completely from `R` home directory; you can
try: remove.packages("rtracklayer"). Don't be panic, if this problem still
bumps up again, try to reboot your PC (you may need to restart your PC
This is an ERROR with rtracklayer until the ERROR is resolved in rtracklayer
you will continue to see this ERROR in your package. We are in the processes of
resolving and should be correctly shortly.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatisti
On 03/29/2017 09:32 AM, Vladimir Kiselev wrote:
Hi Wellinton,
As far as I know if you wrap you shiny stuff into an R function that should
be enough. Then you can provide both non-interactive and interactive
functions and the user can choose what to run.
You can have a look at my SC3 package whe
That is correct. When the Biostrings package is corrected this ERROR in your
package should resolve automatically.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
It's actually an error in rtracklayer.
On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori
wrote:
> That is correct. When the Biostrings package is corrected this ERROR in your
> package should resolve automatically.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
Thanks for the quick reply. Will i need to bump the version to trigger a
rebuild once the changes are made?
On 29 Mar 2017 5:17 pm, "Jurat Shayidin" wrote:
> Hi:
>
> This happened to me several times, and I figured out the issue. I tried to
> remove `rtracklayer` package completely from `R` home
For the single package builder: Once the issue is resolved you could kick off a
new build by bumping the version number; it is probably the fastest way. I will
also try to check and manually build packages that encountered this error and
haven't kicked off a new build.
Lori Shepherd
Bioconduc
Dear Bioconductor Developers,
More news about the Git transition plan. We are coming close to our transition
date and have made significant progress in getting our new server ready for the
Bioconductor community.
1. Overall plan:
- Bioconductor hosts each package as a distinct repository at
g
Hello all,
I think that I'm running into a similar problam as Brad:
If I try the link
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IPO/
for my package IPO, I'm prompted to insert my login-data. Readonly works as
expected. But with my username t.riebenbauer (and th
On Wed, Mar 29, 2017, at 11:23 AM, Martin Morgan wrote:
> On 03/29/2017 09:32 AM, Vladimir Kiselev wrote:
> > Hi Wellinton,
> >
> > As far as I know if you wrap you shiny stuff into an R function that should
> > be enough. Then you can provide both non-interactive and interactive
> > functions and
Thank you all for the recommendations. It is very interesting to know how
other developers are using Shiny.
I have been working on a Shiny application and I did some decisions on code
that are similar to your recommendations:
Separate app into three files to reflect the MVC (Model, View, Controll
Thanks. I have a few thoughts and questions in order to plan ahead:
> - Our plan is to make a 'clean' transition from SVN to git, approximately one
> month after the next Bioconductor release. Developers or users will not have
> access to the SVN system after the date of transition.
In order t
Dear annotation contributors,
Just a reminder the deadline to update annotation packages is Friday
April 7. Please make updated packages available via dropbox or another
location that allows wget. Indicate if the old version should be
included in the upcoming release or if the new package should r
Bioc developers,
R emits a warning when a condition test has length > 1
$ R --vanilla
> if (letters == "a") TRUE
[1] TRUE
Warning message:
In if (letters == "a") TRUE :
the condition has length > 1 and only the first element will be used
These are almost always programming errors.
R-3-4-bran
On 03/29/2017 05:37 PM, Martin Morgan wrote:
Bioc developers,
R emits a warning when a condition test has length > 1
$ R --vanilla
if (letters == "a") TRUE
[1] TRUE
Warning message:
In if (letters == "a") TRUE :
the condition has length > 1 and only the first element will be used
These are
Hi Martin,
On 03/29/2017 02:37 PM, Martin Morgan wrote:
Bioc developers,
R emits a warning when a condition test has length > 1
$ R --vanilla
if (letters == "a") TRUE
[1] TRUE
Warning message:
In if (letters == "a") TRUE :
the condition has length > 1 and only the first element will be use
Hi,
I am writing the following command and get the following error.
Can you please look into the issue ?
> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===]
[ ChAMP.LOAD START >]
---
Thanks for the clarification. Now everything is ok except the check in Linux
(http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/malbec2-checksrc.html).
The package 'ggforce' is not preinstalled in Linux (others seem fine).
Best, Hai
Sent from my iPhone
> On 29 Mar 2017, at 17:17, Micha
Hi Martin,
Not sure what happened during automatic installation of CRAN package
pcalg by the build system on malbec2 but it seems that the installed
package ended up being in a broken state. I just went on malbec2 and
re-installed the package by hand so normally epiNEM should look all
green on Fr
Hi Hai,
Looks you added CRAN ggforce recently (in February) to the Suggests
field of Pi. ggforce depends on CRAN package udunits2, which itself
requires system library libudunits2 in order to compile on Linux,
which itself can be installed with
sudo apt-get install libudunits2-dev
on Debian/U
Dear Yuan Tian,
Thank you very much for your mail .
I have already add a session info with the previous mail.
Problem arise in your script "champ.load.R" line 70 ( bc=beadcount(rgSet) ).
"beadcount" belongs to package "wateRmelon".
In "beadcount" function from line 3 (nb <- assayDataEleme
Thanks Herve for resolving it. Best, Hai
Sent from my iPhone
> On 30 Mar 2017, at 06:42, Hervé Pagès wrote:
>
> Hi Hai,
>
> Looks you added CRAN ggforce recently (in February) to the Suggests
> field of Pi. ggforce depends on CRAN package udunits2, which itself
> requires system library libudu
On 03/27/2017 09:43 AM, Michael Lawrence wrote:
I committed a fix into R trunk with a regression test.
Thanks Michael. Any chance you can port the fix to the 3.4 branch?
H.
On Mon, Mar 27, 2017 at 8:41 AM, Michael Lawrence wrote:
My bad guys, I'll fix when I get to work.
On Mon, Mar 27,
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