filtered to contain just
the most recent version of each. Does it matter then what order the
repositories are visited?
Martin Morgan
From: R-package-devel on behalf of Greg
Hunt
Date: Sunday, March 31, 2024 at 7:35 AM
To: Dirk Eddelbuettel
Cc: List r-package-devel
Subject: Re: [R-pkg-devel] Order
Actually BiocManager delegates to remotes, and remotes is only a 'Suggests', so
the user needs to have both remotes and BiocManager
pkgs <- c("remotes", "BiocManager")
pkgs <- setdiff(pkgs, rownames(installed.packages())
install.packages(pkgs)
and then
BiocManager::install("/")
or
or (`n`
partially matches `na.print`, and 2 is not a valid value); both methods
silently ignore the typo print(m = 2).
Martin Morgan
From: R-devel on behalf of Henrik Bengtsson
Date: Tuesday, February 6, 2024 at 4:34 PM
To: Izmirlian, Grant (NIH/NCI) [E]
Cc: r-devel@r-project.org
Sub
. And an exploratory
https://github.com/Bioconductor/bioc2u; I don't know the status of that project.
At some point the scale tips from installing packages from standard
repositories to using a local clone
https://bioconductor.org/about/mirrors/mirror-how-to/.
Martin Morgan
From: R-package-devel
also need to make a change for tcrossprod…)
Martin Morgan
From: Bioc-devel on behalf of Zuguang Gu
Date: Tuesday, January 16, 2024 at 11:49 AM
To: Zhigang Li
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] IFAA Bioconductor
I saw MatrixExtra defines several S4 methods/dispatches
CRAN knows about Bioconductor packages, so add phyloseq to Depends: , Imports:,
or Suggests: as appropriate.
These CRAN packages seem to Import phyloseq, for instance
> db = available.packages(repos = "https://cloud.R-project.org;)
> rownames(db)[grepl("phyloseq", db[,"Imports"])]
[1]
Using setRepositories()does not give the correct repositories for all
Bioconductor releases. For instance, the R-4-3 version might be associated with
Bioconductor 3.17 (the �previous� release) or 3.18 (the �current� release). R
thinks Bioc 3.17 is appropriate (not wrong, just not correct)
>
at the R-SIG-mac mailing list might have been more
appropriate, but I did not see the issue discussed there.
Martin
From: Prof Brian Ripley
Date: Wednesday, May 31, 2023 at 3:46 AM
To: Martin Morgan
Cc: Tomas Kalibera , R-devel
Subject: Re: [Rd] Building R from source always fails on
tools:::sy
: Tuesday, May 30, 2023 at 4:54 PM
To: Martin Morgan , R-devel
Subject: Re: [Rd] Building R from source always fails on
tools:::sysdata2LazyLoadDB
On 5/30/23 22:09, Martin Morgan wrote:
> I build my own R from source on an M1 mac. I have a clean svn checkout in one
> directory
I build my own R from source on an M1 mac. I have a clean svn checkout in one
directory ~/src/R-devel. I switch to ~/bin/R-devel and the first time run
cd ~/bin/R-devel
~/src/R-devel/configure --enable-R-shlib 'CFLAGS=-g -O0'
CPPFLAGS=-I/opt/R/arm64/include 'CXXFLAGS=-g -O0'
make -j
At some
I opened two issues for further discussion of the technical aspects.
https://github.com/Bioconductor/BiocManager/issues/165
https://github.com/Bioconductor/pkgrevdocs/issues/108
Just to be clear, as noted at the end of the second issue and on the web page
you mention, a Bioconductor package
For off-piste use I would have consulted `setRepositories(graphics = FALSE)`
and then
```
## use Sys.setenv() before setRepositories
Sys.setenv(R_BIOC_VERSION="3.18")
setRepositories(ind = 1:4) # CRAN plus Bioc soft, anno, and expt repos
getOption("repos")# check
CRAN is fine with Bioconductor Depends: and Imports: dependencies, as
previously mentioned. This is because the CRAN maintainers explicitly configure
their system to know about Bioconductor package repositories.
Users face a different challenge -- many users will not have identified (e.g.,
via
The release version DESCRIPTION file is malformed, because it contains a
(partial) merge commit tag
https://code.bioconductor.org/browse/HPiP/blob/RELEASE_3_16/DESCRIPTION#L69
Martin
From: Bioc-devel on behalf of matine rb
Date: Tuesday, April 4, 2023 at 3:00 PM
To: bioc-devel@r-project.org
Martin
From: Robert Castelo
Date: Wednesday, March 29, 2023 at 4:08 PM
To: Martin Morgan , bioc-devel@r-project.org
Subject: Re: [Bioc-devel] httr::GET() problem downloading a ExperimentHub
resource
good catch, but really enigmatic, BAI files work, but BAM don't:
dat <-
rea
Not really helpful but this could be simplified a bit by removing the redirect
from experiment hub, and the layer from httr to curl, so
url =
"https://functionalgenomics.upf.edu/experimenthub/gdnainrnaseqdata/LiYu22subsetBAMfiles/s32gDNA0.bam;
curl::curl_fetch_disk(url, tempfile())
Error in
I would not follow the instructions in RTIGER�s README for installing
Bioconductor packages.
BiocManager::install(�RTIGER�) would install both CRAN and Bioconductor
dependencies of RTIGER, and would be my preferred instruction in a README or
INSTALL file. A complete instruction might be to
If you choose to introduce a second package, I would suggest immediately
deprecating MoonlightR. The two versions co-exist for a development and release
cycle for comparison / opportunity for users to adjust, and then there is only
MoonlightR2.
This avoids confusion for new users. You can
I recently made the change Henrik suggests in the �devel� but not �release�
branch of BiocParallel, so the manuals can be compared. Take a look at the
�Constructor� and �Accessors: Logging and results� sections of the
�SnowParam-class.Rd� man page, starting on p. 53 of the PDF.
I�m not particularly experienced with this but wrote a �proof-of-concept�
skeleton of a package at https://github.com/mtmorgan/ocl . The basics are
* Import OpenCL in the DESCRIPTION file
* Write OpenCL scripts in inst/ (dnorm implemented in OpenCL)
* Use the helper function in
Just my two cents, but I don’t think using `globalVariables()` is a good idea
in a package – it’s too easy to say that R should ignore a variable that it
should not.
In the context of dplyr, the alternative is to `importFrom dplyr .data` or to
use ‘standard’ evaluation, depending on
hu, Jul 7, 2022 at 8:32 AM Giulia Pais wrote:
>
> Thanks for the reply,
>
> By just playing a little with some test code it seems like the approach
> suggested by @Henrik Bengtsson is pretty straightforward so I’ll try with
> this one,
>
> Thanks again to everyone and have a
However, I think it is better to formulate regular expressions to cover
all of Unicode, so do something like e.g. "only keep ASCII digits, ASCII
space, ASCII underscore, but remove all other characters".
Best
Tomas
On 1/4/22 8:35 PM, Martin Morgan wrote:
>
_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.0
(I have built my own R on macOS; similar behavior is observed on a Linux
machine)
Any hints welcome,
Martin Morgan
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Check out grDevices::hcl.pals (also
https://www.zeileis.org/papers/Zeileis+Hornik+Murrell-2009.pdf) or the
RColorBrewer package (also https://colorbrewer2.org) for principled selection
of colors. Sounds like you're interested in 'qualitative' color palletes.
Martin Morgan
On 11/29/21, 4:23
I'm not sure that this is a good idea? For instance R does not set the random
number stream to be the same by default. Not sure what others might think...
Martin
On 11/26/21, 6:01 AM, "Bioc-devel on behalf of Dario Strbenac via Bioc-devel"
wrote:
Good day,
I maintain an R package
Linux and macOS use MulticoreParam() by default, and the 'workers' inherit the
environment (e.g., loaded packages) of the 'manager'. Windows doesn't support
this mode, and instead uses SnowParam() by default; likely you'll be able to
reproduce the error on your system by using SnowParam(),
The problem with using gdb is you'd find yourself in the garbage collector, but
perhaps quite removed from where the corruption occurred, e.g., gc() might /
will likely be triggered after you've returned to the top-level evaluation
loop, and the part of your code that did the corruption might
It is from base R
https://github.com/wch/r-source/blob/a984cc29b9b8d8821f8eb2a1081d9e0d1d4df56e/src/main/memory.c#L3214
and likely indicates memory corruption, not necessarily in the code that
triggers the error (this is when the garbage collector is triggered...).
Probably in *your* C code
Remember that Windows doesn�t have �forked� parallelism; all processes are
running in separate processes where the functions in use need to be made
explicitly available.
Likely you can emulate this error on non-windows by using �SnowParam()� instead
of MulticoreParam(), e.g.,
>
This does sound like a BiocParallel side effect, and I would suggest
holding off for another week so for the BiocParallel changes to be
finalized.
On 9/24/21, 2:05 PM, "Bioc-devel" wrote:
Hello,
My package `clusterExperiment` has not changed but is hitting errors on the
devel branch. I’ve
Errors that are intermittent and platform-specific are often due to memory
corruption, and can be investigated on Linux platforms with valgrind or
similar tools. Have you taken this approach?
On 9/24/21, 3:22 AM, "Bioc-devel" wrote:
Hi,
for several years xcms is suffering from absolutely
mmunity. Anyway, I've been learning a
lot from this discussion. Thanks all!!
Best,
Tiago
Em sex., 3 de set. de 2021 às 12:58, Martin Morgan
<mailto:mtmorgan.b...@gmail.com> escreveu:
The specific repository you've chosen is not what you want to do. This will
always install EBImage from Bioc
repository. That's a lot to tell your users...
Maybe others in the R community have a better way (the key information is in
tools:::.BioC_version_associated_with_R_version(), but that is not an exported
function so not recommended for CRAN packages...)
Martin Morgan
On 9/1/21, 8:13 AM, "
I have options(useFancyQuotes = FALSE) in my ~/.Rprofile.
Martin Morgan
On 7/13/21, 11:37 AM, "R-devel on behalf of Frederick Eaton"
wrote:
Dear R Team,
I am running R from the terminal command line (not RStudio). I've noticed
that R has been using Unicode quo
have any great insight to offer here; superficially it sounds
like the server is sometimes rejecting connections, and these have happened to
line up with OS.
Martin Morgan
On 7/12/21, 8:46 PM, "Bioc-devel on behalf of Paul Shannon"
wrote:
The problem is described in full h
Mousing over the red dot provides an explanation, e.g., for OncoSimulR "NO,
package depends on 'Rgraphviz' which is not available." Rgraphviz is indeed
failing on all three platforms, but from the landing page it has propagated
some time this release for Linux and macOS and so OncoSimulR can
When I try to debug on my macOS, I need to do the following
```
R -d lldb
(lldb) process launch --environment
DYLD_LIBRARY_PATH=/Users/ma38727/bin/R-devel/lib
```
where `/Users/ma38727/bin/` is the location on my system where R is installed.
Martin
On 7/2/21, 11:32 AM, "Bioc-devel on behalf
value section, I think...
627 stats-defunct.Rd stats-defunct arima0.diag FALSE
I guess it makes sense for defunct functions not to be fully documented,
though maybe it would be helpful for those trying to migrate their code...
Martin Morgan
On 6/23/21, 1:58 PM, "
in
From: Oleksii Nikolaienko
Date: Tuesday, May 25, 2021 at 6:28 PM
To: Martin Morgan
Cc: "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] C++ parallel computing
Hi Martin,
thanks for your answer. The goal is to speed up my package (epialleleR), where
most of the functions are al
!) you've tried to implement this in Rsamtools.
Martin Morgan
On 5/24/21, 10:01 AM, "Bioc-devel on behalf of Oleksii Nikolaienko"
wrote:
Dear Bioc team,
I'd like to ask for your advice on the parallelization within a Bioc
package. Please point me to a better place if this ma
of the Bioconductor build system – the lagging package Is
usually promptly updated so the published dependency is satisfied.
From: Henrik Bengtsson
Date: Tuesday, May 18, 2021 at 2:41 PM
To: Martin Morgan
Cc: "Dalgleish, James (NIH/NCI) [F]" ,
"r-package-devel@r-project.org"
Subje
+x86_64 builder mentioned in the post has the wrong
version of rtracklayer for R-devel.
Martin Morgan
On 5/18/21, 11:49 AM, "R-package-devel on behalf of Henrik Bengtsson"
wrote:
It's a problem with Bioconductor and a broken release history of
'rtracklayer' on MS Windows (e.g.
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> > On 11/20
It's because Bioconductor won't be building (supporting) R-4.2 (R-devel) until
six months from now, even in the 'devel' branch of Bioconductor. Bioc 3.14
(once it becomes available after the Bioconductor release) will use R 4.1 and
the table will be updated to have line 34 as 3.14 / 4.1. There
This is because of a change in base R
https://github.com/wch/r-source/blob/9ad27a744572fca453665e97110ded41a2680a57/doc/NEWS.Rd#L257
It can be reproduced by using a recent version R-4-1.
Looking at your code, I guess it is at
s is
enough to cause a fault during package build -- it seems like the code writes
nothing nowhere, but ...
Martin Morgan
On 4/7/21, 8:08 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D."
wrote:
Hi Herv�,
Thank you for the information. I will try to figure out.
Ji
that it will be fixed,
so either be patient or ask the rtracklayer maintainer directly to address this
by, e.g., opening an issue at https://github.com/lawremi/rtracklayer
Martin Morgan
On 4/7/21, 6:32 AM, "R-package-devel on behalf of Gordon Brown"
wrote:
Hi, Rosario,
The message is t
From the Bioconductor 'devel' (3.13, used with R-devel) 'landing page' for
rtracklayer
https://bioconductor.org/packages/devel/rtracklayer
The 'build' badge is red; clicking on it shows a build system problem with
rtracklayer on Windows. Scrolling on the landing page to the bottom shows
This is a known issue and has not yet resolved sorry about that. Martin
On Thu, Mar 25, 2021 at 6:34 AM Bhagwat, Aditya <
aditya.bhag...@mpi-bn.mpg.de> wrote:
> Dear bioc-devel,
>
> Thank you for having autonomics<
> https://bioconductor.org/packages/devel/bioc/html/autonomics.html> on
>
if your examples repeatedly calculate the same thing, and this is also typical
of how users use your package, it might make sense to 'memoise' key functions
in your package https://cran.r-project.org/package=memoise
Martin
On 3/22/21, 7:41 AM, "Bioc-devel on behalf of Kern, Lori"
wrote:
It looks like you're assigning to assays, `assays(x) <- ...`, so you need to
import `assays<-`, and not just `assays`.
But this
assays(new_obj)@listData <-
looks VERY BAD. The internal structure of the assays slot (accessed with @)
should NEVER be accessed directly; use the public 'API'
Have you pushed your changes to git.bioconductor.org? I see
HPAStainR master$ git remote -v
origin g...@git.bioconductor.org:packages/HPAStainR (fetch)
origin g...@git.bioconductor.org:packages/HPAStainR (push)
HPAStainR master$ git pull
Already up to date.
HPAStainR master$ grep Version
If you mean package building on your own machine, you could add the
options(timeout = 300L) to a file
'.Rprofile' in your 'HOME' directory; that way the timeout is set for all your
R sessions, including the one that is building the package.
The Bioconductor build system already has reactome.db
The Bioconductor remote should not include 'ICBI,
git remote remove upstream
git remote add upstream g...@git.bioconductor.org:packages/CINdex.git
On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar"
wrote:
Hello,
We are the package maintaines for the CINdex
This information has not yet been determined. Usually we try to sync with R,
especially in the spring when there is a new, rather than patch, release of R.
R has not announced when their release is (see
https://developer.r-project.org/), so we haven't started our own release
process. Likely it
Your package will build under the new name. When it builds successfully, the
url https://bioconductor.org/packages/VaSP will point to the new landing page.
The user will install it with `BiocManager::install("VaSP")`. The user will use
the package with `library("VaSP")`.
The old version of
in your package NAMESPACE do you importFrom(data.table, ".I") ?
On 2/16/21, 7:52 PM, "Bioc-devel on behalf of Alice Yue"
wrote:
Hello there,
I am working to update the flowGraph package on Bioconductor and I keep
getting an error about a missing namespace for the following code
/bioconductor_docker:devel image was rebuilt from source.
Martin Morgan
On 2/16/21, 7:01 PM, "Bioc-devel on behalf of Robert M. Flight"
wrote:
Hi Catherine,
It looks like igraph is not installed, which RCy3 depends on. This seems
odd, because my own package categoryCompare depen
This seems to be a problem with many newer packages; I'll look into this. It
had been reported (and fixed) previously, but apparently some additional
gremlins have entered the system...
Martin
On 2/12/21, 1:23 PM, "Bioc-devel on behalf of Laurent Gatto"
wrote:
I just realised that the
The error says
unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so':
so it's having trouble loading the openssl R package. There are installation
instructions for this package at
https://github.com/jeroen/openssl#readme
(I
their code wouldn�t be transparent enough. Hopefully I�m not
being hypocritical here.
Martin
From: Ana Carolina Leote
Date: Wednesday, February 10, 2021 at 10:24 AM
To: "Kern, Lori"
Cc: Martin Morgan , Wolfgang Huber
, "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] H
If the package is already widely used, then I guess it provides useful
functionality, and so your package doesn't have to provide that functionality,
so perhaps a better solution is to refer users to the unsupported package in
your vignette??
What you say about not being maintained in over a
It's likely failing because your package has C source code that accesses memory
in an invalid way. Likely the bug is present on all platforms, but only
apparent, for the tests you have written, on Windows. The right thing to do is
to fix the bug, rather than avoid by not running on the
1. New features -- even those that improve the package ;) -- should be added to
devel; your users will have access to them soon enough, and it provides a
chance for the bugs and errors that new code inevitably introduces to be worked
out.
2. If the data is used in the package per se, e.g., in
Is it from lines like this
https://github.com/calabrialab/ISAnalytics/blob/69341f6591c6765a4a70253f7ab85e64cca9845d/vignettes/collision_removal.bib#L18
in your github repository?
Martin
On 2/3/21, 11:32 AM, "Bioc-devel on behalf of Giulia Pais"
wrote:
Hello,
I'm trying to push
The build system tries to behave like a typical *user* system, so it installs
macOS binaries. But for whatever reason, macOS binaries for the 'devel' version
of R seem only to be produced at the last minute leading up to a release. So if
the package you depend on requires compilation, then it
I'd guess that your *docker* system is running out of resources, e.g., memory.
I'm not sure how docker determines memory available, so don't really know how
to solve this other than googling for things like 'how much memory does my
docker image have' and 'how do I allocate more memory to
I am not sure but I think the app is case sensitive, and you have entered
Yuzhou.Chang.
(also, in your email you didn't include the name of your package, which made it
a little harder to track your problem...)
Martin
On 1/8/21, 4:02 PM, "Bioc-devel on behalf of Yuzhou Chang"
wrote:
Hi
Actually, I generate other errors, but not the build report errors.
I see your package git repository includes 'cached' files,
vignettes/fcoex_files; these are not appropriate for a git repository, since
they reflect some state on your particular machine, rather than on the build
system or
On the one hand, if the error is from curl I think this is the case
url <- "localhost:8000" ## nothing to connect to
tryCatch({
response <- GET(url)
stop_for_status(response)
content(response)
}, error = function(e) {
message(paste(class(e), collapse = " "))
stop("curl
bioconda is not maintained by Bioconductor, you should ask through bioconda
support channels
https://bioconda.github.io/
maybe as an issue on their github repository?
Martin
On 11/25/20, 8:36 PM, "Bioc-devel on behalf of CHEN Ying"
wrote:
Hello BioC community,
I have recently
If you have successfully built the vignette, under correct Bioconductor version
and valid installation, then I suggest pushing your changes to the Bioconductor
git repository. The NIGHTLY builds will occur, and with luck they will be
successful and visible in the next build report (either
not sure that this is a good answer or not, but on scanning your vignette I
didn't see any use of LaTeX math expressions, so perhaps mathptmx is not needed
at all in and can be removed from the vignette?
At any rate when I remove it and try
epihet/vignettes master$ R CMD Sweave --pdf
same result with BiocManager::version() 3.13
From: Shraddha Pai
Date: Tuesday, November 24, 2020 at 8:13 AM
To: Martin Morgan
Cc: Bioc-devel
Subject: Re: [Bioc-devel] Running vignettes one at a time works but
build_vignettes causes buffer overflow
Hi Martin,
The issue is on the bioc-devel
It would really help (maybe this has been mentioned before, but I'm not very
good at remembering things) to indicate what package this is!
When R installs a package, it (probably this is not the right thing to do)
builds all vignettes in the same session. Maybe devtools does this too? You
Nice images!
If I narrow the browser window, the figures appear!
When I 'inspect' the source, for instance for 'Figure 4: chance of cross talk'
I see that the image has tag whereas figures that
show up have class="widefigure".
I guess smallfigure is because in the Rmd there is
```{r,
there, too -- it would be worth figuring out before embarking on that
solution.
Because the Bioconductor build system would not build the vignette, the advice
remains that the static vignette should NOT be included in your Bioconductor
package.
Martin Morgan
Bioconductor
On 11/13/20, 7:13 AM
I'm looking for...
Martin Morgan
On 11/11/20, 4:44 PM, "R-package-devel on behalf of Duncan Murdoch"
wrote:
Here's what I think is happening.
In the movMF:::.onLoad function there's a test whether flexmix is
installed. If found, then it is loaded and some methods are
y
standard guidance/vignette for how Rhtslib & Rhdf5lib approached this? There
are numerous Rcpp vignettes that I could find, but couldn't find for pure C
compiled by R?
________
From: Martin Morgan
Sent: Saturday, November 7, 2020 3:30 PM
To: Alexa
It would probably help to provide additional detail here; there are several
examples of packages that build C / C++ libraries from source, a common pattern
is to have a package dedicated to providing the library, e.g., Rhtslib or
Rhdf5lib, or of building the library as part of the software
...it would be useful to know whether 'timeout' settings, e.g., options(timeout
= 180) improves things. I've introduced pull request on BiocManager to do this,
at
https://github.com/Bioconductor/BiocManager/pull/81
Martin
On 11/5/20, 11:04 AM, "Martin Morgan" wrote:
I noticed in Johannes' message
> In addition: Warning messages:
...
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
> URL
'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/msdata_0.31.0.tar.gz':
Timeout of 60 seconds was reached
I looked at
FWIW BiocManager::install() really delegates to install.packages(). The
packages are downloaded to 'destdir=' as documented on ?install.packages --
typically file.path(tempdir(), "downloaded_packages") -- and one path to
troubleshooting installs is to tackle the problematic installation(s)
I made sure I was using Bioc-3.13 and that my packages were valid
> BiocManager::version()
[1] '3.13'
> BiocManager::valid()
[1] TRUE
I then ran purl() and source(), eventually arriving at the error on the build
system
> knitr::purl("multiGSEA.rmd")
[1] "multiGSEA.R"
> source("multiGSEA.R",
Thanks; the version of BiocManager in git has
> library(BiocManager)
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
and will be released in the next month. The rationale for telling you
(csym, psym);
+ UNPROTECT(1);
}
return class;
}
seems to remove the warning; I'm guessing that the other SEXP already exist so
don't need protecting?
Martin Morgan
On 10/29/20, 12:47 PM, "R-devel on behalf of luke-tier...@uiowa.edu"
wrote:
Yes, if
git remote -v
lists something like
famat master$ git remote -v
upstream g...@git.bioconductor.org:packages/famat (fetch)
upstream g...@git.bioconductor.org:packages/famat (push)
then `git push upstream master` will push the changes on your current local
branch to the
I believe that NanoporeNSeq was added to the experiment data build 'manifest'
after the most recent build (on Mondays and Thursdays) started, so it will not
be available until Monday experiment data package builds are complete, and
bambu has been built with those packages available -- I think
Your NAMESPACE has
import(ComplexHeatmap)
...
import(pheatmap)
and both packages have a function pheatmap -- the import from ComplexHeatmap is
being replaced by the import from pheatmap.
In other places your NAMESPACE has lines like
import(seqinr, except = c(zscore, count, a))
so you'd like
from, but I don't have easy access to a Windows
machine for this type of work.
Martin Morgan
On 10/16/20, 7:00 PM, "Bioc-devel on behalf of Gordon K Smyth"
wrote:
This is more an R question than a Bioconductor question, but I would be
grateful if the Biocore team or other Bioc
Packages are built nightly, so you must usually wait ~24 - 48 hours for your
commits to be reflected in the build report.
Sometimes issues prevent the build report from being processed, so on the build
overview page such as
http://bioconductor.org/checkResults/devel/bioc-LATEST/
compare
3.11 is the current release version. Commits to the current release version
were disabled yesterday.
https://bioconductor.org/developers/release-schedule/
You want to push changes to the devel ('master') branch.
Martin
On 10/14/20, 5:34 AM, "Bioc-devel on behalf of Laure Cougnaud"
This warning
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Athaliana.TAIR.TAIR9’
means that you have used BSgenome.Athaliana.TAIR.TAIR9 in your code, but you
have not declared it in your DESCRIPTION file, either as Imports: or Suggests:.
Since
The version scheme is outlined at
https://bioconductor.org/developers/how-to/version-numbering/
Within a 'release', the version x.y.z is always bumped in the z field. You are
at 1.8.0 in release, so the version bump is to 1.8.1, 1.8.2, ...
Meanwhile, in devel you were at 1.9.0, so the version
The message is trying to say that RCurl has not been declared in the
DESCRIPTION file; add Imports: RCurl to the DESCRIPTION.
I know that you indicate that you have done this already, but it is not present
in the current DESCRIIPTION file, and it is the reason for the current warning
message.
seq2pathway
R CMD check seq2pathway_.tar.gz
?
Martin Morgan
On 10/1/20, 12:27 PM, "Bioc-devel on behalf of Yuxi Sun"
wrote:
Hi,
I am writing on behalf of the development team for the package seq2pathway.
After updating to python 3 and replacing the deprecated i
yes Hervé has made this point too -- mucking with the history of the package,
potentially breaking historical checkouts (when large files are deleted from
the history, too).
It's relevant because when a package is added to our repository we do a full
clone of the master branch; an alternative
uot;, "numeric"))
Error in setOldClass(c("character", "numeric")) :
inconsistent old-style class information for "character"; the class is
defined but does not extend "numeric" and is not valid as the data part
In addition: Warning message:
In .validDat
te
'not yet initialized' and distinct from character(0) or NA_character_, but want
to mention those often appropriate alternatives.
With
setClassUnion("maybeNumber", c("numeric", "logical"))
every instance of numeric _is_ a maybeNumber, e.g.,
> is(1, &qu
1 - 100 of 1367 matches
Mail list logo
