Also perhaps using BiocFileCache so that the result object is only generated
once, then cached for future (different session) use.
On 12/18/18, 8:35 AM, "Bioc-devel on behalf of Michael Lawrence"
wrote:
I would recommend against dependencies across vignettes. Ideally someone
can pick
this comes from `findGlobals()`
> foo <- `[`
> findGlobals(foo)
Error in makeUsageCollector(fun, ...) : only works for closures
> traceback()
4: stop("only works for closures")
3: makeUsageCollector(fun, ...)
2: collectUsage(fun, enterGlobal = enter)
1: findGlobals(foo)
In the bigger context it
different vignette in the same
build session, but this gets back to the problem of ensuring that the result
object is generated by one vignette before it is needed by another vignette.
> >
> > -A
> >
> > > On 18 Dec 2018, at 14:14, Martin Morgan mailto:mtmorgan.b...@gmail.com>> wrote
lue))
>> findGlobals(value)
>> else character(0)
>> })
>> 3: findLogicalRdir(pkgname, c("T", "F"))
>
> Change is.function(value) to typeof(value) == "closure" and you should be
OK.
>
>
rce and some related questions
(Shepherd, Lori)
3. Re: Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0
(Martin Morgan)
4. Re: Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0
(Tierney, Luke)
5. Re: Compilation flags,
It seems like you've posted this in several locations -- stackoverflow, slack,
here. Choose one forum and stick with it, so that people do not waste their
time duplicating effort. Regardless of forum, provide a minimal reproducible
example (e.g., a stripped-down github repository) to illustrate
A good place to start is to verify that your packages are all from the same
release
BiocManager::valid()
and then if that is not revealing make sure to start a new R session, attach
SummarizedExperiment, and report the output of sessionInfo().
Martin
On 12/1/18, 8:16 PM, "Bioc-devel on
RCurl_1.95-4.11yaml_2.2.0
[10] compiler_3.6.0 GenomeInfoDbData_1.2.0
Let me know if you see a potential fix.
Best,
Lan
On Sun, Dec 2, 2018 at 9:38 AM Martin Morgan
wrote:
A good
I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
shortly.
I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
> library(BiocParallel)
> set.seed(1); p = bpparam(); rnorm(1)
[1] -0.6264538
> set.seed(1); p = bpparam(); rnorm(1)
[1]
On 3 Jan 2019, at 14:00, Martin Morgan wrote:
>
> This seems to be a regression in R-devel, and has been reported.
>
> Previously (at least svn r75833, I think)
>
> df <- data.frame(vers= package_version("1.2"))
> rbind(df, df)$ve
This seems to be a regression in R-devel, and has been reported.
Previously (at least svn r75833, I think)
df <- data.frame(vers= package_version("1.2"))
rbind(df, df)$vers
returned
[1] '1.2' '1.2'
now (r75945) we have
> rbind(df, df)$vers
[[1]]
[1] 1 2
[[2]]
[1] 1 2
Martin
On
Memory use can be complicated to understand.
library(BiocParallel)
v <- replicate(100, rnorm(1), simplify=FALSE)
bplapply(v, sum)
by default, bplapply splits 100 jobs (each element of the list) equally between
the number of cores available, and sends just the necessary data
48453 -0.48906078 0.43304237 -0.03195349
[10] 0.14670372
> unlist(bplapply(1:4, rnorm, BPPARAM=SnowParam(4, RNGseed=123)))
[1] -0.96859273 -0.40944544 0.89096942 -0.48906078 0.43304237
-0.03195349 -1.03886641 1.57451249 0.74708204
[10] 0.67187201
Best,
The location is driven primarily by willingness of local organizers to
host; there is no current location set for BioC2020, so if you're
interested...
Martin
On 09/12/2018 07:08 PM, Stephanie M. Gogarten wrote:
Are there any plans to have another BioC on the west coast in the near
future?
1E# service=git-upload-pack
0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'" >
I wrote about this a couple of days ago and received the response
"
Martin Morgan
Sep 9, 2018, 12:47 PM (3 days ago)
to me, bioc-devel
I'd guess that your remote is incorrect;
On 09/15/2018 12:34 PM, Levi Waldron wrote:
John, is your new version number reflected on the devel version of the
package landing page and the build report? After you push a new version
number to master, it will propagate the next day after overnight
building/testing.
AFAIK, there are only
If users trying to install the package from the release branch would be
unable to do so, then yes you should update the release.
Martin
On 09/17/2018 06:23 AM, Francesco Ferrari wrote:
Dear Lori,
I already foxed the issue in the devel branch which now gives a clean check:
I added a response to your issue at
https://github.com/Bioconductor/Contributions/issues/1002#issuecomment-478991986
encouraging you (again) to avoid installing software on the user system; there
are basic problems with this approach, and the correct solution is to list
kallisto as a
/packages/3.9/workflows;
CRAN
"https://cran.rstudio.com;
>
On 3/25/19, 7:42 AM, "Martin Morgan" wrote:
I think the usual incantation in configure files is ${R_HOME}/bin/R ...
R_HOME is the path to R set by the command that starts
I think the usual incantation in configure files is ${R_HOME}/bin/R ... R_HOME
is the path to R set by the command that starts to build or install the
package, whereas Rscript is found on the search path.
Martin
On 3/25/19, 7:33 AM, "Bioc-devel on behalf of Vincent Carey"
wrote:
The
The original discussion which made me think it's not permissable is here:
https://github.com/Bioconductor/Contributions/issues/985#issuecomment-468003572
Thanks again,
Steve
From: Martin Morgan
Sent: Th
Lots of package do this so probably you're missing a step, e.g.,
import(Biostrings) or importClassesFrom(Biostrings, DNAStringSet).
What makes you think it's not permissible?
Martin
On 4/3/19, 1:19 AM, "Bioc-devel on behalf of Stephen Martin Pederson"
wrote:
Hi,
I'm really
Thank you, this regression is fixed in 1.17.16.
Martin
On 2/24/19, 1:07 AM, "Bioc-devel on behalf of Yinan Zheng"
wrote:
Hi Bioc-Devel team,
I am trying to fix the build error of my package "REMP" on BioC 3.9
(http://bioconductor.org/checkResults/devel/bioc-LATEST/REMP/).
In today's R-devel, I install packages required for the vignette, including
CNVRanger's Suggests: packages, and ensure that my installation is valid
(modulo some irrelevant packages) via BiocManager::valid().
I then Stangle'd the vignette
cd CNVRanger/vignettes
R CMD Stange CNVRanger.Rmd
blob_1.1.1
#> [35] magrittr_1.5 promises_1.0.1
#> [37] htmltools_0.3.6 mime_0.6
#> [39] interactiveDisplayBase_1.21.0 xtable_1.8-3
#> [41] httpuv_1.4.5.1stringi_1.3.1
#> [43] RCurl_1.95-4.12
Created on 20
Aaron points in the right direction with generating random number streams in
the serial part of the program, then sending these to the workers in a
consistent way. Use ?nextRNGStream to generate the streams for each replicate,
and .Random.seed on the thread. Probably this generates a BiocCheck
Issues with the SPB may persist until Tuesday morning. Martin
On 2/18/19, 5:29 AM, "Bioc-devel on behalf of Felix Ernst"
wrote:
Hi,
I just wanted to ask, whether the SPB is under maintenance.
After a push, the bot reports the start of a build, but
Several research groups affiliated with Bioconductor received seed funding to
develop software for access to and analysis of Human Cell Atlas data. We're
having a 'virtual symposium' to summarize our work in progress on 20 February,
12pm Eastern time. Please feel free to join!
More
use `globalVariables()` to declare these symbols and quieten warnings, at the
expense of quietening warnings about undefined variables in _all_ code and
potentially silencing true positives. Avoid non-standard evaluation (this is
what ddply is doing, using special rules to resolve symbols like
It's important to distinguish between problems in your code and problems in the
tools (or use of tools) to process the code. Here the use of setGeneric() /
setMethod() is correct. Your use of roxygen2 is getting in the way.
You've used @rdname to document the methods on the same page (reducing
I think the best / only way to do this is to convince the author that this type
of self-promotion is not helpful in the long run --- if all maintainers did
this then a typical R session would start with 10's of these, and each would
have no impact.
Martin
On 2/16/19, 2:35 PM, "Bioc-devel on
These users have been added manually. If others have similar problems please do
let us know (a common problem is that the confirmation email gets classified as
'spam', but that seems not to be the case here). Martin
On 2/19/19, 2:45 PM, "Bioc-devel on behalf of Lily Wang"
wrote:
Dear
methods for the exact signature one wishes to
support, rather than allowing any kind of inheritance / dispatch.
Martin Morgan
On 1/29/19, 12:10 PM, "Bioc-devel on behalf of Pages, Herve"
wrote:
Hi Martin.
Speed is not the concern: I just did some quick benchmarki
To change the email address associated with this mailing list, visit
https://stat.ethz.ch/mailman/listinfo/bioc-devel
and click on the button that says 'unsubscribe or edit options'. Follow the
on-screen steps.
Martin
On 1/25/19, 2:50 AM, "Bioc-devel on behalf of Minoo Ashtiani"
wrote:
A simple approach is to suppress the message (I think this is pragmatic, rather
than dumb __) about unknown class (along with DESCRIPTION Suggests: Seurat)
setGeneric("getGE", function(x) standardGeneric("getGE"))
suppressMessages({
setMethod("getGE", "seurat", function(x)
Printing from multiple workers to stdout is problematic anyway, because the
output from different workers is not intrinsically synchronized -- they will
appear interleaved with each other.
Generally for forked processes connections (to stdout, files, databases, urls,
...) need to be opened on
Hi Chengyang -- welcome!
1. yes, there can be multiple commits and then a bump of z. Only when z is
incremented does a new version propagate from the build system to the public
repository available to end users. It is probably best practice to bump the
version z on every commit -- there is no
The function needs to be exported from the name space, and documented. Since
you're using roxygen2, the relevant tag is
#' @export
above the definition of the function.
Martin
On 4/8/19, 4:00 PM, "Bioc-devel on behalf of margaret linan"
wrote:
Hi -
Can anyone tell me how to
The app and package were associated with your svn account; I have updated the
app to know about your current email address; you should be able to request a
password reset and add ssh keys.
Martin
On 4/8/19, 6:19 PM, "Bioc-devel on behalf of Hannes Hettling"
wrote:
Dear Bioconductor
Your configure outsmarts the check system, so your options are to omit the
flags or to live with the warning. Either solution is fine with Bioconductor.
Martin
On 4/12/19, 4:17 AM, "Bioc-devel on behalf of Jochen Knaus"
wrote:
Hi everybody,
for our new R package "Netboost" we
I second the idea of reproducing with the Windows build commands, which have to
do more than 'just' build for a particular architecture. One might test the
hypothesis that it is staged install that is causing the problem with
StagedInstalll: no
in the DESCRIPTION file.
Makevars is
Your strand factor only has level "+", but should have levels "+", "-", "*".
Use GenomicRanges::strand() to construct the right thing.
Martin
On 4/14/19, 3:01 AM, "Bioc-devel on behalf of Dario Strbenac"
wrote:
Good day,
Although the documentation states "Generally not used
Core packages go through the same review process as community contributed
packages, although many of the core packages pre-date the current github review
process.
Github seems to have been introduced in 2016. Before that we used the roundup
issue tracker system where packages were uploaded and
Mostly the build system tries not to be fancy; make sure that you've got the
correct version of R and Bioconductor and your packages are up-to-date
BiocManager::install(version="3.10")
BiocManager::valid()
and that you're working with the correct code
cd /tmp
git clone
mclapply is not available or documented on Windows. I think the solution is
actually to be vague, and replace \code{\link[parallel]{mclapply}}) with
\code{\link{mclapply}} at
https://github.com/sellerslab/gemini/blob/b1408bdce22df08d6950fee578eaac7665f54960/R/gemini_parallelization.R#L9
Martin
6/17/19, 4:11 PM, "Sidharth Jain" wrote:
Makes sense for mclapply, I'll remove the links in the documentation.
What about `%<>%` from magrittr? From my recollection, it should also be
available on Windows machines.
Thanks,
Sid
I think it has to do with the use of reference classes in the assay slot, which
have different environments
se = SummarizedExperiment()
saveRDS(se, fl <- tempfile())
se1 = readRDS(fl)
and then
> all.equal(se@assays, se1@assays)
[1] "Class definitions are not identical"
>
Steffi
> On April 12, 2019 at 1:10 AM Martin Morgan
wrote:
>
>
> That easy strategy wouldn't work, for instance two successive calls to
MulticoreParam() would get the same port assigned, rather than the contract of
a 'random' port in a specif
I tried to reproduce the commands reported by the build system. So on a fresh
git clone
$ cd /tmp
$ git clone g...@git.bioconductor.org:packages/trena
$ R -vanilla CMD build --keep-empty-dirs --no-resave-data trena
(the buld system doesn't use vanilla, but I have an ~/.Rprofile and maybe
), starting
with our May, 2019 meeting.
See also the support site NEWS posting
https://support.bioconductor.org/p/121130/ .
Martin Morgan
Bioconductor
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
It's not appropriate to 'split' your package between the bioconductor git
repository and other locations on the internet; you should carefully revise
your vignette to convey high quality information within the constraints of
Bioconductor's guidelines.
Martin
On 4/30/19, 1:55 PM, "Bioc-devel
s bioc-3.9
alias bioc-3.9='R_LIBS_USER=~/Library/R/3.6/Bioc/3.9 ~/bin/R-3-6-branch/bin/R'
but other solutions are possible
Martin Morgan
On 5/7/19, 5:06 AM, "Bioc-devel on behalf of Miles Benton"
wrote:
I had the same issue today, here's the note I made on our work Teams
cha
rce, with appropriate --prefix
to keep your
installation sandboxed in ~/bin?
Andrew McDavid
Biostatistics and Computational Biology
Office: SRB 4.206 Ph: 585.275.5983
Message: 1
Date: Tue, 7 May 2019 10:46:49 +
From: Martin Morgan
To: Miles Benton , Felix E
posted and answered on the support site
https://support.bioconductor.org/p/122277
Martin
On 6/26/19, 6:38 AM, "Bioc-devel on behalf of lejeczek via Bioc-devel"
wrote:
hi devel
where is 3.9 version?
It is not in CRAN that's for sure.
...
selection: 1
Under bioc-devel, I ran
MACPET/vignettes$ R CMD Stangle MACPET.Rmd
and then in R
source("MACPET.R", echo = TRUE)
where the problem manifests as
> summary(MACPET_pintraData,heatmap=TRUE)
Error in .Vector_summary(object, ...) : unused argument (heatmap = TRUE)
You have the S4 class
>
t 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 messa
Hi Doug -- I'll clean this up, and will let you know when we're back on track.
Martin
On 4/25/19, 5:31 PM, "Bioc-devel on behalf of Doug Barrows"
wrote:
Hello,
Tom Carroll and I recently had a package, profileplyr, accepted on
Bioconductor. When trying to push a few minor
maybe as an aid to debugging this, after running R CMD check on
_1.5.1.tar.gz one can run just the examples with
R -f pkg.Rcheck/pkg-Ex.R
or interactively with something like
R
> source("pkg.Rcheck/pkg-Ex.R", echo = TRUE, max = Inf)
Martin
On 4/17/19, 5:31 AM, "Bioc-devel on behalf of
.snowPort() make a copy of .Random.seed (if it exists) before
calling runif() and restoring it on exit.
H.
On 4/11/19 15:25, Martin Morgan wrote:
> This is actually from a dependency DelayedArray which, on load, calls
DelayedArray::setAutoBPPARAM, which calls
This is called the 'tragedy of the commons', where everyone seems something
that looks good (screen real-estate to advertise their package) and so takes
advantage of it. Once everyone does that, the 'commons' is completely destroyed
by messages like the one you're trying to suppress.
You can
also remember that you are making changes to the _devel_ version of
Bioconductor, so must look for changes in the devel branch of the repository;
http://bioconductor.org/developers/how-to/useDevel/
Martin
On 7/15/19, 9:28 AM, "Bioc-devel on behalf of Shepherd, Lori"
wrote:
We will
Do you think this approach could be re-cast in the same way that
https://github.com/Bioconductor/bioconductor_full has done, so that the
container has all the software to _support_ the packages needed for the jupyter
notebook, but that the user must do some kind of initialization to install the
gt; *From:* Pages, Herve
> *Sent:* Wednesday, August 21, 2019 7:47 PM
> *To:* Zhezhen Wang ; Martin Morgan
> ; Vincent Carey
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] BiocCheck error
> Note that the name of the package (BioTIP) differs from
I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
at package status. Likely there are issues accessing these sites
(BiocManager::repositories()) from your computer. It seems not to be an issue
that you as developer need to worry about, provided you are confident that
can you provide an example of the samtools command line that you evaluate?
On 8/23/19, 6:11 PM, "Bioc-devel on behalf of Jonathon Hill"
wrote:
I had not until today. I spent the afternoon looking at the possibility,
and it looks like it would be beyond my lab’s skills. We do not have
quot;--min-BQ", minBaseQuality(param),
> "--region", as.character(chrRange, ignore.strand=TRUE))
>
> As you can see, we use the BAQ score to filter. We have tried to
implement it without BAQ (using Rsamtools) and found it negatively affected o
es/M3C.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/M3C.git'
Chris
On Thu, 5 Sep 2019 at 11:17, Martin Morgan wrote:
This seems like a bug in the
Putting bioc-devel back in the loop.
I think that the straight-forward answer to your original query is 'no, git
modules are not supported'.
I think we'd carry on and say 'packages should be self-contained and conform to
the Bioconductor size and time constraints', so you cannot have a very
This seems like a bug in the version check code.
The next number after '999' is '1000', but '9991' is larger than '999', too, so
I think both 1000 and 9991 are valid version bumps; '10' is less than '999' so
is not a valid version bump.
Note that .99... has no special significance in the third
This conversation has moved to the community-bioc slack, where the
recommendation is to use BiocFileCache to manage the download. Martin
On 7/29/19, 10:42 AM, "Bioc-devel on behalf of Shraddha Pai"
wrote:
Hi,
Our software package relies on a Java jar file that is 11Mb in size and
://support.bioconductor.org/p/121130/
[2]: https://forms.gle/zTZLZJQrHL4ZGEGq9
[3]: https://bioc-community.herokuapp.com/
Martin Morgan
Bioconductor
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Bioc devel prepares for the next release of bioc, using the version of R that
will be closest to that in use at the time of the release.
The version of R that will be in use at the time of the next bioc release will
be R-3.6.*.
You should be using R-3.6 for bioc-devel.
This is summarized at
Windows (and macOS) CRAN packages are installed as binaries (as experienced by
the typical user), so don't need compilation-- Rstan is built by CRAN through
whatever magic / agreement.
The paragraph at the very end of
Oops, I said 'vignettes' but meant the reference manual. Html vignettes (from
appropriate Rmd files) are have been available for a number of years.
Martin
On 9/25/19, 5:10 PM, "Martin Morgan" wrote:
Our recollection is that there is no 'flag' in R CMD build to create HTML
r
Sorry, this should be included in the builds tonight for release tomorrow. I'll
update the release announcement when the package becomes available. Martin
On 10/31/19, 3:09 PM, "Bioc-devel on behalf of Oriol Senan Campos"
wrote:
Dear list members,
First of all congratulations
If it were me I might update version
BiocManager::install(version="3.10")
...
Update xxx packages [y/n]: n
Confirm I've got the right version
BiocManager::version()
and then recover the URLs
BiocManager::repositories()
as arguments to install.packages(). It doesn't make sense to ask for
On the 3_9 branch I see
commit c1382c3f7a0e3872cb66d077f9572b2b9618ecec (HEAD -> RELEASE_3_9,
origin/RELEASE_3_9)
Author: Ting Huang
Date: Sat May 4 16:12:18 2019 -0400
Update version bump
commit 21273e6d818ed70fd258a9574700cc0f53ce0b8b
Author: Ting Huang
Date: Thu Aug 22 01:08:03
Update your installation
BiocManager::install(version = "3.10")
or see the vignette browseVignette("BiocManager") section 'Managing multiple
versions" to manage multiple installations (in case you need to reproduce
existing workflows).
Martin
On 11/13/19, 11:07 AM, "Bioc-devel on behalf
I think it is this
https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you
should just sit tight...
On 12/5/19, 7:39 AM, "Bioc-devel on behalf of Kevin RUE"
wrote:
Hi,
I've been getting a weird Latex-related error on the daily build recently,
_although I
Pleaae try again; there is inconsistent logic when adding some maintainers with
github id and existing packages. Martin
On 10/28/19, 5:52 AM, "Bioc-devel on behalf of Anand MT"
wrote:
Dear mods,
Recently our package `methrix` (https://github.com/CompEpigen/methrix) got
accepted
sorry, forgot to push the commit! please try again... Martin
On 10/28/19, 9:43 AM, "Anand MT" wrote:
I tried several times, but no luck. Still lacks write permissions
From: Martin Morgan
Sent: 28 October 2019 18:20
A preliminary insight is that it looks like you're using R-devel (aka R-4.0),
whereas at the moment (until the next Bioconductor release in a couple of
weeks...) the 'supported' devel version of Bioconductor uses R-3.6.*.
Martin
On 10/17/19, 10:10 AM, "Bioc-devel on behalf of Zhu, Jack
It's hard to tell from the stack trace, but is this reproducible in a new R
(devel) session with
loadNamespace("ensembldb")
? And did you actually install new packages in R-devel, or only re-use packages
installed in an earlier version of R? If the latter, then definitely you'll
want to
You're using R-devel, whereas Bioconductor is using R-3.6.x for both our
release and devel branches. Consequently, you're being required to compile from
source, rather than using the pre-built binaries. For this reason, your system
needs to have the necessary libraries and their headers; this
rather than aiming for an a large ExperimentData package it might make more
sense to create an ExperimentHub package, with the data hosted in the cloud for
download-on-demand. It is cached locally so the download cost is only paid
once. This is especially useful if your data consist of several
The rationale is that bpiterate() is used when the number of iterations is
unknown (hence the length of the progress bar indeterminate...), whereas
bplapply() is a more natural candidate for iteration when the length of the
iteration is known... is bpiterate() providing functionality (REDUCE,
Thanks for that insight, we'll try to solve the issue with BiocStyle.
Martin
On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay"
wrote:
I’ve been getting the exact same error for compiling the Rmarkdown
vignettes in my own package. Some partial testing before
Thanks this seems like a problem with large file size on Windows, probably in
Rhtslib.
It might be better practice and more reliable to use BiocFileCache for
downloads, e.g.,
url =
Often this means that there is some resource in your vignette that has not been
terminated correctly, e.g., a parallel process that has not be stopped or a
graphical device that is still open.
Martin
On 9/25/19, 4:46 AM, "Bioc-devel on behalf of Alberto Valdeolivas"
wrote:
Hello all,
Our recollection is that there is no 'flag' in R CMD build to create HTML
rather than PDF vignettes; without that it would be non-trivial to create html
output, e.g., links across pages. (I *think* the installed package html help
pages are generated on the fly...)
What is your experience with
I think this is an error in BiocParallel that has been corrected (in v. 1.19.4)
but not yet propagated through the build system and report.
Martin
On 10/11/19, 7:33 PM, "Bioc-devel on behalf of Christian Mertes"
wrote:
Dear Bioc Team,
I noticed already the error and I'm not
I wonder what your package is?
On 10/12/19, 3:19 PM, "Bioc-devel on behalf of Graw, Stefan H"
wrote:
Dear devel team,
How do I correctly make changes to my package that got accepted and is
currently in the devel version?
Thank you for your help,
It seems like in your vignette you are trying to install your own package. But
if you needed to install the package, then the vignette wouldn't be available
to install it from... ;) In this code chunk
```{r results='hide',message=FALSE,warning=FALSE}
if (!requireNamespace("BiocManager", quietly
I'd guess that 'car' is trying to use globalVariables() with saying Imports:
utils in the DESCRIPTION and / or importFrom(utils, globalVariables) in the
NAMESPACE?
Martin
On 12/19/19, 2:22 PM, "Bioc-devel on behalf of Vincent Carey"
wrote:
I can't get a handle on this apparent issue
I checked out your package
git clone https://git.bioconductor.org/packages/anamiR
and then, on R-devel (since that is the version being used in the current
Bioconductor 'devel' release) and with BiocManager::version() returning 3.11
and BiocManager::valid() returning TRUE, I did
cd
20, 2019 at 5:08 PM
To: Martin Morgan , "Shepherd, Lori"
Cc: "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] Trigger a new build after version bump
Thank you, Martin!
It worked exactly as you mentioned. Now the package has been built
successfully, except for windows o
ebruary 24, 2020 at 10:31 PM
To: Martin Morgan
Cc: Bioc-devel
Subject: Re: [Bioc-devel] Deleting netDx.examples package from BioC
Hi Martin,
Great, thank you. I will set the number of cores to one for the examples (must
have had something running in parallel).
I was unable to find the BioC g
Once a version has been made 'public', it's not possible to go backward -- R
will say 'hey, you've got version 1.99.0 installed, so that's more recent than
1.13.0, so I won't update it'. So you're stuck with the version going forward.
Martin
On 3/3/20, 10:14 AM, "Bioc-devel on behalf of
You can't use a package version other than the current release, so
BiocNeighbors needs to be updated (assuming that's the problem); I'm sure it
will be. Martin
On 2/28/20, 2:51 AM, "Bioc-devel on behalf of Leonardo Collado Torres"
wrote:
Hi,
When installing BiocNeighbors
rse
this; in the future only incorporate bug fixes in the release branch.
Martin Morgan
Bioconductor
On 1/23/20, 11:09 PM, "py11" wrote:
Hi Lori,
I just pushed my new updated package into RELEASE_3_10 with version
1.2.3(old one was 1.2.1); however, I didn't s
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