Hi,
Sounds good- that's something I haven't run. I ran R CMD check after adding
the .Rcheck file with BioC flags but this sounds different.
But will look up how to run this.
Thanks, Herve.
Shraddha
On Fri, Jun 14, 2019 at 8:02 PM Pages, Herve wrote:
> Sounds good. Also don't forget to run 'R
> What about Atom, VS Code and the like? Or what about taking a project
> that meets most of the constraints and pushing to cover all of them,
> or even forking it and modifying the part you don't like?
I'm not prepared to endorse GitHub affiliated software.
[[alternative HTML version
Sounds good. Also don't forget to run 'R CMD BiocCheck' on the source
tarball of the package. Right now it reports a lot of problems:
hpages@spectre:~$ R CMD BiocCheck netDx_0.99.0.tar.gz
...
Summary:
ERROR count: 3
WARNING count: 7
NOTE count: 12
Once everything is ready,
Hi,
Ok thank you.
I should probably comment out some time-consuming steps in the vignettes
and just include the output in the companion data set, read those in.
Thanks, will do that before next push to master.
Best S
On Fri, Jun 14, 2019 at 7:37 PM Pages, Herve wrote:
> On 6/14/19 15:58,
On Sat, 15 Jun 2019 at 01:24, Abby Spurdle wrote:
>
> None of the tools that I've looked at satisfy these constraints.
> But if you know of some, I'd like to know... And I would consider
> contributing...
What about Atom, VS Code and the like? Or what about taking a project
that meets most of
On 6/14/19 15:58, Shraddha Pai wrote:
> Hi,
>
> Thanks Herve. I have actually spent weeks making sure my packages passed
> check and build following guidelines. So I am actually doing my best and
> your snarky remark is not appreciated.
OK maybe. But please note that our guidelines say that
On Fri, Jun 14, 2019 at 7:24 PM Iñaki Ucar wrote:
>
> There are many similar projects that are mature
I'm not sure what projects you're referring to.
If we create some constraints:
(1) Internal systems consoles (*plural*).
Rules out most things.
Noting that many tools are designed to bypass
Hi,
Thanks Herve. I have actually spent weeks making sure my packages passed
check and build following guidelines. So I am actually doing my best and
your snarky remark is not appreciated.
Then at the very end I expanded the DESCRIPTION file by putting in line
breaks in the "description" field,
Hi,
From the Linux command line:
git clone https://github.com/BaderLab/netDx
R CMD INSTALL netDx
* installing to library ‘/home/hpages/R/R-3.6.r76454/library’
Error: error reading file '/home/hpages/sandbox/netDx/DESCRIPTION'
R CMD build netDx
* checking for file
Hello BioC dev community,
I just submitted a package to BioC.
1) The automatic build gave it an "ABNORMAL" status with the following
error " Accessing git_info complete. get_dcf_info failed; could not open."
https://github.com/Bioconductor/Contributions/issues/1149
I've Googled a bit and cannot
Yes. You identified it a while ago and Deepayan wrote that he fixed it on
r-forge a year ago. It still isn't on cran.
On Fri, Jun 14, 2019 at 16:04 Duncan Murdoch
wrote:
> On 14/06/2019 9:12 a.m., Richard M. Heiberger wrote:
> > This is still not repaired in
> > R version 3.6.0 Patched
On 14/06/2019 9:12 a.m., Richard M. Heiberger wrote:
This is still not repaired in
R version 3.6.0 Patched (2019-05-17 r76528)
library(latticeExtra)
a <- xyplot(1 ~ 1)
c(a,a)
Warning message:
In formals(fun) : argument is not a function
Can we have it in R-3.6.1 that Peter just announced?
Hi,
It seems like the email is configured correctly on BiocCredentials app. It is
because the account is not activated it doesn't work. You'd have to first
activate your account before moving forward with setting a password.
I've added your GitHub credentials to the account.
Best,
Nitesh
Hi,
I'd like to update my package Clonality
https://bioconductor.org/packages/release/bioc/html/Clonality.html
I used to do it through svn but as I understand it's not possible now.
I can't connect it to my git page with updated package
https://github.com/IOstrovnaya/Clonality
When I enter
Thank you. We will investigate further and let you know when we have a solution
on our end.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From:
The advantage of "abort" (R_Suicide) over the default (R error) is that
it cannot be caught accidentally, so that one can detect more errors,
and it may be easier to find where the error happened. To make the
default behavior less surprising/more user friendly, and to allow
intentional
It looks like for arch'x64', there is no package org.Hs.eg.db.
Following is the whole error message:
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
trackViewer-package 22.44 0.07 24.88
viewTracks 13.97
On 14 June 2019 at 15:22, arnaud gaboury wrote:
| I have build R with Intel MKL.The libraries are free for one year (maybe
| did it change). The build is far from being trivial. Please find on my
| github[0] some details
Gee, when oh when does this "meme" of "I built R with MKL" die?
It is for a long time. Since last development version (BioC 3.9).
Jianhong.
From: "Shepherd, Lori"
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via
Bioc-devel
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10
How long as this ERROR occurred?
I just went
How long as this ERROR occurred?
I just went onto tokay1 and was able to run library("org.Hs.eg.db") with no
issues. Let's wait and see if it clears up on todays build report. If not we
will investigate further.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
On Fri, Jun 14, 2019 at 1:44 PM lejeczek via R-devel
wrote:
> On 13/06/2019 16:14, Dirk Eddelbuettel wrote:
> > On 13 June 2019 at 16:05, lejeczek via R-devel wrote:
> > | I'd like to ask, and I believe this place here should be best as who
> can
> > | know better, if building R with different
This is still not repaired in
R version 3.6.0 Patched (2019-05-17 r76528)
> library(latticeExtra)
> a <- xyplot(1 ~ 1)
> c(a,a)
Warning message:
In formals(fun) : argument is not a function
Can we have it in R-3.6.1 that Peter just announced?
Rich
On Mon, Apr 2, 2018 at 4:08 AM Deepayan
On 14/06/2019 14:43, Frank Schwidom wrote:
Hi John,
First, the unix and linux filesystem allows the use of any nonzero character in
its filesystem filenames
Well, even it's not the central point of the discussion let make this
assertion more correct. It depends on file system. E.g. JFS
Hi John,
First, the unix and linux filesystem allows the use of any nonzero character in
its filesystem filenames and the c functions open / fopen, symlink. rename,
chdir and so on don't care about any tilde. If the open systemcall gets a file
which begins with a tilde then it will try to
On 13/06/2019 16:14, Dirk Eddelbuettel wrote:
> On 13 June 2019 at 16:05, lejeczek via R-devel wrote:
> | I'd like to ask, and I believe this place here should be best as who can
> | know better, if building R with different compilers and opt flags is
> | something worth investing time into?
> |
Full schedule is available on developer.r-project.org.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
On 14/06/2019 5:04 a.m., Michael Gruenstaeudl wrote:
Assume an R package (`myRpackage`) that has a conda package
(`condaDependecy`) as a system requirement. The file `DESCRIPTION` of
the R package would read like:
Package: myRpackage
...
SystemRequirements: condaDependecy (>=
Assume an R package (`myRpackage`) that has a conda package
(`condaDependecy`) as a system requirement. The file `DESCRIPTION` of
the R package would read like:
Package: myRpackage
...
SystemRequirements: condaDependecy (>= 0.1)
...
How can I ensure the automatic installation
Honestly, I don't see the motivation for this. There are many similar
projects that are mature, so my feedback would be: don't reinvent the wheel
and contribute to those.
Iñaki
El vie., 14 jun. 2019 3:18, Abby Spurdle escribió:
> I thought that I'd get more feedback.
> But it's ok, I
We have recently repurposed the scRNAseq package to serve as a general
location for any publicly available single-cell count data. The aim of
this package is to provide convenient functions that directly yield
nicely formatted SingleCellExperiment objects containing count matrices
and relevant
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