This problem has been recognized:
https://github.com/cboettig/knitcitations/issues/107
In a few days it will likely clear.
On Wed, Nov 25, 2020 at 10:26 PM Eeles, Christopher <
christopher.ee...@uhnresearch.ca> wrote:
> Hello Bioc community,
>
> I am the maintainer for PharmacoGx and have
my email "topics sought ..." was not intended for this list, but i welcome
direct
contact from anyone who is interested in it
--
The information in this e-mail is intended only for the ...{{dropped:18}}
___
Bioc-devel@r-project.org mailing list
Hi -- I know this is an inopportune moment for many but I just wanted to
reach out to the TAB to ask for topics of interest. Mike Love and
colleagues
will be discussing *Hubs in the TAB talk section, but there is time for
other
concerns. We do plan to discuss handling .github/workflow folders in
le error. Anyway, there isn't a current version on
> Github (there is a two-year old version at github.com/cran/RCurl), so
> there isn't a more interactive way to report the error.
>
> On Mon, Nov 23, 2020 at 12:20 PM Vincent Carey
> wrote:
>
>> I reproduced the problem yo
I reproduced the problem you noted. Rebuilding RCurl with (an updated?)
openssl for
windows is not a slam-dunk for me at the moment. Can the curl package do
what you need?
On Mon, Nov 23, 2020 at 11:49 AM James W. MacDonald wrote:
> FYI, there appears to be a problem with RCurl on Windows,
RCurl was originally an omeghat offering by Duncan Temple Lang. I have a
windows
machine here and will have a look.
On Mon, Nov 23, 2020 at 11:49 AM James W. MacDonald wrote:
> FYI, there appears to be a problem with RCurl on Windows, most likely due
> to building against an old version of
ug report / feature
> request (e.g., via `bug.report()`).
>
> Martin
>
> On 11/4/20, 1:19 PM, "Bioc-devel on behalf of Vincent Carey" <
> bioc-devel-boun...@r-project.org on behalf of st...@channing.harvard.edu>
> wrote:
>
> I certainly have run into this s
s are the packages that have failed to install on
> first pass.
>
> It does seem like this would be a reasonable feature for base R, that we
> could inherit, so one could ask on R-devel or submit a bug report / feature
> request (e.g., via `bug.report()`).
>
> Martin
>
> On 1
On Sun, Nov 8, 2020 at 7:40 AM Alexandru Voda
wrote:
> Thanks for the reply, Martin!
>
> Unfortunately, the C++ software is large (
> https://ctg.cncr.nl/software/magma), not just some feature that can be
> used from R base, CRAN or Bioconductor.
>
just having a quick look at magma source --
I certainly have run into this situation with R generally. It seems like a
patch to
install.packages would be the best approach to introduce this
functionality. I wonder
if Henrik Bengtsson or Dirk Eddelbuettel have pondered this.
In any case, I am sympathetic with the suggestion but I believe
Here's what happened when I tried to build your package as instructed in
the report page:
stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES$ R_ENVIRON_USER=~/.Renviron.bioc
Rdev CMD build multiGSEA
1/9 packages newly attached/loaded, see sessionInfo() for details.
* checking for file ‘multiGSEA/DESCRIPTION’
You can install the package, using current R, from the source image at
https://bioconductor.org/packages/3.1/bioc/src/contrib/inSilicoDb_2.4.1.tar.gz
I did this
Then I tried to use it
> getPlatformList()
*Error: Webservice not accessible. Please check your internet connection.:
Error in
On Mon, Oct 19, 2020 at 1:41 PM Martin Morgan
wrote:
> Just to respond that I don't have a clear answer for you; I would guess
> that there is a change upstream of your package, and that the NOTE is
> spurious. If this also occurs on a non-Bioconductor Windows machine then it
> would be
forwarding to bioc-devel
-- Forwarded message -
From: Vincent Carey
Date: Mon, Oct 19, 2020 at 6:33 AM
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
To: Manders-2, F.M.
Cc: Alessandro Lussana via Bioc-devel
looks like BiocCheck/checks.R
entrum.nl> wrote:
> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t
> know why I have an X there and not a number.
>
>
>
> *From: *Vincent Carey
> *Date: *Monday, 19 October 2020 at 12:20
> *To: *"Manders-2, F.M."
> *Cc: *Alessandro Luss
person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl",
role = c("aut"),
comment = c(ORCID = "-0001-6197-347X")),
is what I see in a current checkout. is "X" at the end correct? maybe
there is an encoding issue?
On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <
Bioconductor has published a project-wide code of conduct:
http://bioconductor.org/about/code-of-conduct/. We invite all members of
the community to familiarise themselves with it.
The Bioconductor community values
- an open approach to science that promotes the sharing of ideas, code,
and
Thanks Jiefei! I wanted to acknowledge Conrad's comments too -- we will
discuss them as a group in our monthly technical advisory board meeting to
assess adequacy of documentation and support resources for conditions
like these. Our project must make use of a variety of technologies to meet
the
Starting from
PairwiseAlignments-class package:Biostrings R Documentation
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and
PairwiseAlignmentsSingleSubjectSummary objects
Description:
The ‘PairwiseAlignments’ class is a container for storing a set of
pairwise
This should probably be posed to the support site. What version of the
package are you using? Where
are you seeing coordinates? I would expect those to be obtained from the
TxDb package, or perhaps
from AnnotationHub.
> columns(org.Dr.eg.db)
[1] "ACCNUM" "ALIAS""ENSEMBL"
it folder. I'll use the
> Bioconductor version and we don't need to dig more since this version
> works. Still, very strange situation.
>
> Thanks again,
> Mikhail
>
> On Sat, Aug 8, 2020 at 7:12 AM Vincent Carey
> wrote:
>
>> Hi Mikhail -- I cannot reproduce your pr
Hi Mikhail -- I cannot reproduce your problem. I think I need more details
as to how
your error is triggered. Using rcmdcheck::rcmdcheck within R as shown in
this transcript,
on the built tar.gz from the current git checkout master branch, I have
── R CMD check results
Hi Mikhail -- would you provide the results of sessionInfo() after the
failure? Thanks
On Fri, Aug 7, 2020 at 7:08 PM Mikhail Dozmorov
wrote:
> Dear Bioconductor team,
>
> I am trying to update a package we developed, HiCcompare.
> https://bioconductor.org/packages/HiCcompare/. The package has
Can you post an example dataset that triggers the error reproducibly?
On Tue, Jul 14, 2020 at 4:44 AM Charles Plessy
wrote:
> Hello,
>
> a user of the CAGEr package reported an error that occurs when it calls
> the `export.bw` function of rtracklayer:
>
> rsession: 1730343 1730344 doesn't
RCurl_1.98-1.2 tibble_3.0.1
> [40] ggdendro_0.1-20tidyr_1.1.0crayon_1.3.4
> [43] pkgconfig_2.0.3MASS_7.3-51.5 ellipsis_0.3.1
> [46] data.table_1.12.8 rstudioapi_0.11R6_2.4.1
> [49] compiler_4.0.0
>
>
> On Wed, 17 Jun 2020 at 20:12
I can reproduce the error, which arises from iheatmapr. Note that
http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec1-R-instpkgs.html
shows that iheatmapr is 0.4.12 and on my system example(iheatmap) fails
with the
error you showed. In future please provide sessionInfo() result when
Eye color")$SNPS)
> eyersids
> [1] "rs12913832" "rs7173419" "rs3002288" "rs12896399" "rs1408799"
> [6] "rs12520016" "rs288139" "rs1667394" "rs4596632" "rs12203592"
> [11
I am really sorry about the situation with gwascat and will try to
straighten it out today.
On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo
wrote:
> hi,
>
> my package GenomicScores is not building, see:
>
>
>
On Wed, Jun 3, 2020 at 11:48 PM stefano wrote:
> Hello Community,
>
> I am used to document function although hey are not exported
>
>
I suppose you are talking about tidybulk? I am somewhat mystified by the
behavior
of
%vjcair> R CMD build tidybulk
* checking for file ‘tidybulk/DESCRIPTION’
hi stefano
what package are you talking about, what is the exact error message you
are concerned about (please transcribe or copy exactly) and what version of
R are you working with?
thank you
On Wed, Jun 3, 2020 at 11:48 PM stefano wrote:
> Hello Community,
>
> I am used to document
f appearing out of nowhere. For examples, I
> >> actually only see advantages of not using lazyData, because of these
> >> explicit statements.
> >>
> >> My historical impression: I would say that when lazyData was
> introduced,
> >&g
LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
&
This file trips up fread around record 170349, inconsistently ... I haven't
figured that out yet.
readLines, strsplit may be the ultimate solution.
On Thu, Apr 30, 2020 at 7:15 AM Vincent Carey
wrote:
> right, line 35265 of
> http://www.ebi.ac.uk/gwas/api/search/downloads/alternati
o be a
> problem.
>
> If you point to the location of the file I could investigate further...
>
> Martin
>
> On 4/30/20, 6:55 AM, "Bioc-devel on behalf of Vincent Carey" <
> bioc-devel-boun...@r-project.org on behalf of st...@channing.harvard.edu>
> wrote:
>
The EBI GWAS catalog is large -- now the download is over 100MB for 179K
associations. A "bug" in the
package was reported, so I acquired the file by hand.
> nn = read.delim("gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv",
sep="\t")
*Warning message:*
*In scan(file = file, what = what,
I see this is guideline 7 at
https://bioconductor.org/developers/package-guidelines/
I have used LazyData: TRUE so that [pkgname]::[entity] can be used instead
of data(). The
claim that it is "rarely a good thing" and slows down package loading can
be weighed against
convenience. I am not sure
I will chime in because the error is a bit obscure. You serialized
ExpressionSet instances for testing. In the expected_res
in your tests we have
..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1
slot
.. .. ..@ .Data:List of 4
.. .. .. ..$ : int [1:3] 3 6 1
..
I think "header says it all" may be intended ... the question is whether
it is accepted. since the package seems to be in error state I am not sure
it can move forward at this time
On Tue, Mar 24, 2020 at 8:22 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> Is there a question
I am weak on finding logs, but at
https://github.com/Bioconductor/Contributions/issues?q=is%3Aissue+is%3Aopen+tidybulk
I see the package is in an error state. Can you fix that?
On Tue, Mar 24, 2020 at 7:31 AM Stefano Mangiola
wrote:
>
> ___
>
I just updated my R and I am getting into trouble with MLInterfaces
maintenance.
> BiocManager::install("MLInterfaces")
*Bioconductor version 3.11 (BiocManager 1.30.10), R Under development
(unstable)*
* (2020-03-15 r77975)*
*Installing package(s) 'MLInterfaces'*
*Warning: unable to access
On Mon, Mar 9, 2020 at 6:58 AM Roman Hillje via Bioc-devel <
bioc-devel@r-project.org> wrote:
> Hi all,
>
> I was wondering if there is a class for results of differential gene
> expression analysis. I couldn’t find anything generic. Perhaps it’s too
> similar to a simple data frame, but I like
This has been a very interesting and illuminating dialogue but it really
should be moved to
support.bioconductor.org so that a record is available to the general user
community.
The solution here
> library(Homo.sapiens)
Error in library(Homo.sapiens) :
there is no package called ‘Homo.sapiens’
for Android <https://aka.ms/ghei36>
>
> --
> *From:* Bioc-devel on behalf of
> Vincent Carey
> *Sent:* Saturday, March 7, 2020 12:58:57 PM
> *To:* Ulrich Bodenhofer
> *Cc:* bioc-devel@r-project.org ; Kurt Hornik <
> kurt.hor...@wu.ac
I have a feeling that the best way to get action here will be to file an
issue
and perhaps a PR at https://github.com/Bioconductor/Biostrings
On Sat, Mar 7, 2020 at 7:12 AM Ulrich Bodenhofer
wrote:
> Dear colleagues,
>
> As noted in my previous message, I have encountered problems with the
>
~~~
>
> here i'm using the release version of R because otherwise, as i said
> before, some of the function calls to the 'itdepends' package break.
>
>
> i'd be happy to pull-request this code, with the necessary adaptations,
> wherever the community feels is more appr
On Sat, Feb 8, 2020 at 12:02 PM Martin Morgan
wrote:
> I find it quite interesting to identify formal strategies for removing
> dependencies, but also a little outside my domain of expertise. This code
>
It would be nice to collect the ideas in this thread into some
recommendations. The themes
. In fact I already added it as issue into Github
> https://github.com/stemangiola/ttBulk/issues/6
>
> At the moment I have a custom validation function
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The W
You'll need a current version of R and the AnnotationHub package
installed. Then
> library(AnnotationHub)
ah *5/39 packages newly attached/loaded, see sessionInfo() for details.*
> ah = AnnotationHub()
*snapshotDate(): 2019-12-26*
> query(ah, "sativa")
AnnotationHub with 7 records
#
On Sun, Jan 5, 2020 at 7:50 AM Tang, Wenhao
wrote:
> Hello,
>
> I am following this instruction to fix bugs:
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>
> However, both master and RELEASE_3_10 branches were not updated. For
> master branch, I have the
gt; Thank you very much for your response. I really appreciate it.
>
>
>
> How can I define those vectors in my package? Another R script that
> possesses only
>
> all the vectors? Which also needs documentation. Am I correct?
>
>
>
> Best regards,
>
> Arman
&
On Mon, Dec 30, 2019 at 9:35 PM Arman Shahrisa
wrote:
> Hi to all,
>
> I’m the maintainer of the package cbaf. The package relies on various
> terms to find
> the cancer studies that possess specific data e.g. RNA-Seq.
>
> These terms are used by three various functions. I was wondering maybe it
.
The error messaging seemed strange, because there are no problems
loading/checking car on its own
> Martin
>
> On 12/19/19, 2:22 PM, "Bioc-devel on behalf of Vincent Carey" <
> bioc-devel-boun...@r-project.org on behalf of st...@channing.harvard.edu>
> wrote
I can't get a handle on this apparent issue with 'car' -- there is some
indication of this globalVariables error at
https://rdrr.io/github/hadley/tibble/f/revdep/problems.md but I don't see
an explanation. The pernicious aspect of this, which seems limited
to mac, is that it stops the
On my mac and linux systems I am seeing a new
error. With the latest checkout of BiocStyle
rmarkdown::render("foo/BiocStyle/vignettes/AuthoringRmdVignettes.Rmd",
BiocStyle::pdf_document())
produced
! Undefined control sequence.
l.56 \bioctitle
[]{Authoring R Markdown
I tried an inline png but I think it was rejected by bioc-devel. Here's
another try.
On Fri, Dec 13, 2019 at 11:40 AM Vincent Carey
wrote:
> Thanks -- It is good to know more about the complications of adding
> seqlevelsStyle elements.
> I am not sure how pervasive this will
I raised this issue previously with little response.
I'd propose that we add a column or two to genomeStyles()$Homo_sapiens
> head(genomeStyles()$Homo_sapiens, 2)
circular auto sex NCBI UCSC dbSNP Ensembl
1FALSE TRUE FALSE1 chr1 ch1 1
2FALSE TRUE FALSE2 chr2 ch2
The RangedData objects are still viable with the software you are using,
but trying
to set colnames will trigger an error. In Bioc 3.11 you won't even be able
to use
the RangedData class at all. So an intervention is needed now.
The RangedData objects that were serialized or created in your
clang 6 with full path
>
> /usr/local/clang6/bin/clang --version
> clang version 6.0.0 (tags/RELEASE_600/final)
> Target: x86_64-apple-darwin18.7.0
> Thread model: posix
> InstalledDir: /usr/local/clang6/bin
>
> On Wed, Dec 4, 2019 at 11:03 AM Vincent Carey
> wrote:
When installing packages from source,
I frequently run into this error with
%vjcair> clang --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir:
en/curl/issues/209#issuecomment-542758288> •
> edited
>
> On Windows you have to wait for the next release of the r package
>
> https://github.com/jeroen/curl/issues/209#issuecomment-542758288
>
> Greetings
>
> Florian
> Am 23.10.19 um 21:23 schrieb Vincent Carey:
May I ask what is the resolution here? I have updated curl and httr on my
windows box and continue
to see errors unique to windows when requests lack the protocol in the URL.
On Wed, Oct 23, 2019 at 7:28 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> Thank you for the update.
>
>
>
> Andrzej
>
> On Wed, Oct 9, 2019 at 12:10 PM Vincent Carey
> wrote:
>
>> Just wondering whether this has been followed up. I am still seeing build
>> errors for
>> windows related to this.
>>
>> On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes
>&
ick? That's news to me, but I am not following this closely.
>
> On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve <mailto:hpa...@fredhutch.org> > wrote:
>
> On 9/11/19 00:50, Vincent Carey wrote:
> > I seem to be running into a similar problem with BiocOncoTK on
&
I seem to be running into a similar problem with BiocOncoTK on windows
The build report for tokay1 shows:
Loading required package: ontologyIndex
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
how about TF for platforms that support it and C++ for those that don't,
eventually
migrating away from C++ as support grows? a little messy for the moment
but let's
get some mileage on the TF solution ASAP
On Thu, Sep 5, 2019 at 9:21 AM Dirmeier Simon wrote:
> Hi Herve,
>
> > All this means
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error
On Sat, Aug 17, 2019 at 4:40 AM Venu Thatikonda
wrote:
> Hi,
>
> As the title says, is %>% acceptable in bioc packages? With BiocCheck, I
> get a WARNING that is "Add non-empty \\value sections to the following man
> pages: man/pipe.Rd".
>
Yes magrittr is acceptable. The warning says (I think)
t version of the repository.
>
> https://github.com/ohlerlab/RiboseQC/
>
>
> <https://github.com/ohlerlab/RiboseQC/settings>
>
> On Mon, Aug 5, 2019 at 1:22 PM Vincent Carey
> wrote:
>
>> Is there an open github repository where this can be examined as a work
On Thu, Aug 1, 2019 at 10:36 PM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com> wrote:
> One possibility is that this is due to a regression in
> SingleCellExperiment, caused by the altexp updates and other
> refactoring. This should be fixed in 1.7.3, you can check this for
> yourself by
Hi Doug,
I think you've written a method of "[" for class "profileplyr" that is
using certain aspects of the Assays API that
are not guaranteed to be stable. It would be good to have a simple
reproducible example -- I can run
your vignette and see that certain uses of "$" cause errors but
It should be possible to get stringdist as a binary package for mac.
provide your sessionInfo().
> BiocManager::install("stringdist")
*Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 Patched
(2019-05-06*
* r76460)*
*Installing package(s) 'stringdist'*
*trying URL
The error reported by the build system is reproducible on my mac running R
CMD check on
banocc_1.8.0.tar.gz
The check error is pretty terse. I turned your vignette into
an R script using knitr::purl and ran into
> compiled_banocc_model <- rstan::stan_model(model_code =
banocc::banocc_model)
remedied by installation of latest S4Vectors/SummarizedExperiment from git
On Wed, Jun 12, 2019 at 10:53 AM Vincent Carey
wrote:
> my installation of Bioc 3.10 passes valid()
>
>
> > ee = SummarizedExperiment(assay=data.matrix(mtcars))
>
> > ee
>
> class: Summa
my installation of Bioc 3.10 passes valid()
> ee = SummarizedExperiment(assay=data.matrix(mtcars))
> ee
class: SummarizedExperiment
dim: 32 11
metadata(0):
assays(1): ''
rownames(32): Mazda RX4 Mazda RX4 Wag ... Maserati Bora Volvo 142E
rowData names(0):
colnames(11): mpg cyl ... gear
Loading required namespace: HDF5Array
Error in .stop_if_bad_dir(dir, prefix) : directory
"/home/biocbuild/bbs-3.10-bioc/R/library/BiocSklearn/hdf5/tenx_750"
does not seem to contain an HDF5-based SummarizedExperiment object
previously saved with saveHDF5SummarizedExperiment()
Calls: ->
her to much.
>
> Cheers,
> Andrzej
>
> On Mon, May 6, 2019 at 9:42 PM Vincent Carey
> wrote:
>
>> *I don't often compile vignettes to pdf ... but a recent attempt led to:*
>>
>>
>> *Warning message:*
>>
>> *LaTeX Warning: You have re
*I don't often compile vignettes to pdf ... but a recent attempt led to:*
*Warning message:*
*LaTeX Warning: You have requested package
`/Library/Frameworks/R.framework/Vers*
*ions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',*
* but the package provides
Has this situation been rectified?
On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel <
daniel.vantw...@roswellpark.org> wrote:
> We've made some changes to our annotation generation scripts this release
> and it seems these may have introduced some errors. Thank you for
> identifying this issue
On Sun, Apr 14, 2019 at 6:30 PM Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Good evening,
>
> I am having problems with downloading the package used to generate
> regression models on R. The following is the error message I received. I
> tried installing BiocManager instead as
On Wed, Mar 27, 2019 at 9:05 AM Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> On Wed, Mar 27, 2019 at 1:06 AM Aaron Lun <
> infinite.monkeys.with.keyboa...@gmail.com> wrote:
>
> > > well, we can't fix this in old branches of Bioc.
> >
> > Sure, but one could say that about
Morgan" wrote:
>>
>> I think the usual incantation in configure files is ${R_HOME}/bin/R
>> ... R_HOME is the path to R set by the command that starts to build or
>> install the package, whereas Rscript is found on
The error on linux for 3.9:
##
##
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RBGL
###
Guidelines on this topic do not seem to be present in our web
site; there is a link to Wickham's guide but I don't see that it
confronts the topic. I will make some unofficial and possibly
wrong remarks.
Suppose my function has to create a file "foo.txt". If I do it
in the working folder, I
put ggplot2 in Suggests:
see 1.1.3 of https://cran.r-project.org/doc/manuals/r-release/R-exts.html
The ‘Suggests’ field uses the same syntax as ‘Depends’ and lists packages
that are not necessarily needed. This includes packages used only in
examples, tests or vignettes (see Writing package
Can you provide the repo for your package in development? These BiocCheck
issues are important and
should be resolved at your end. We can give some advice on how to get
better results with BiocCheck.
On Wed, Nov 28, 2018 at 10:34 AM Casper Peters wrote:
> So in the package I'm developing, I
I also attempted to replicate and I found that one of your serialized data
elements (eveLocus)
was a GRanges that needed updateObject
However I would like to raise a question about this:
if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
if
The following comes up in use of Fdb.InfiniumMethylation.hg19::getPlatform
debug: mcols(GR)$channel <- Rle(as.factor(mcols(GR)$channel450))
Browse[3]> system.time(uu <- Rle(as.factor(mcols(GR)$channel450)))
user system elapsed
0.020 0.003 0.022
Browse[3]>
>> > To generate mouse.rda, I used:
>> >
>> > library(rtracklayer)
>> > mouse <- readGFF("
>> > ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/
>> Mus_musculus.GRCm38.93.chr.gtf.gz
>> > ")
>> >
>> > An
(resending with reply all -- please reply to this one)
Can you say some more about the content of the file? Perhaps it can be
placed in ExperimentHub. "mouse.rda" is not very descriptive. is it
in your github repo?
On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk
wrote:
> I need to
elevant functionality?
You would get best guidance if you identified a github repo where your
package is being developed. If you are concerned about exposure, you can
invite a developer as a confidential evaluator/consultant. I would be
willing
to play this role if necessary.
Sincerely,
Vincent Care
As Lori has noted Bioconductor users have access to many chain files
through AnnotationHub -- please
let us know if these are not sufficient for your needs.
> library(AnnotationHub)
> ah = AnnotationHub()
> query(ah, "chain")
AnnotationHub with 1513 records
# snapshotDate(): 2018-08-01
#
add something like this
vignette: >
%\VignetteIndexEntry{[your index entry]}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
to your vignette YAML ... see 1.4.2 of
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-package-vignettes
On Fri, May 11, 2018
How about a google drive? This problem of autodownloading should be
addressed directly.
These facilities are still important but their maintenance is clearly a
lower priority as the
technologies handled have diminished use in the field. I think we should
be able to team up and remove
yes, the [] is a habit i need to break. ok, we'll get by.
On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
>
>
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morga
ve to admit to changing the text of the warning with this
>>> commit
>>>
>>>
>>> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11e
>>> e2440fbde891cba524e
>>>
>>> but what I was intending to do was to change what it s
supports a 'package' attribute on the character
>> vector, abstracted by packageSlot().
>>
>>
>>
>> On Thu, Apr 12, 2018 at 3:26 PM, Vincent Carey
>> <st...@channing.harvard.edu> wrote:
>>
>>> If we need to disambiguate class references, perh
If we need to disambiguate class references, perhaps an operator
could help? Along the lines of base::"::" ...
"%c%" <- function(package,class) {
pk = as.character(substitute(package))
cl = as.character(substitute(class))
getClass(cl, where=getNamespace(pk))
}
Biobase %c%
stemsbiology.org>
wrote:
> Hi Vince,
>
> My dumb mistake, sorry. Now fixed, version 0.99.9,
> https://github.com/paul-shannon/IGV
>
> I’m looking forward to hearing your suggestions.
>
> - Paul
>
>
>
> > On Apr 9, 2018, at 4:49 PM, Vincent Carey <st...@cha
Hi Paul -- I am trying to build your vignette but it has
load("~/s/work/priceLab/AD/tbl.gwas.level_1.RData")
I think it should be possible to get your package through
check, but I would like to get the vignette built and
check out the tests before commenting further.
On Mon, Apr 9, 2018 at
ive seen this too apropos bigrquery on windows
On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
wrote:
>
> Dear All,
>
> Two packages I maintain are showing, in Windows, a warning during check
> with messages like
>
> Rd warning:
>
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