Re: [Bioc-devel] RCurl on Windows

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,

Re: [Bioc-devel] 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

Re: [Bioc-devel] Would it make sense for BiocManager::install to cache downloaded packages?

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

Re: [Bioc-devel] Would it make sense for BiocManager::install to cache downloaded packages?

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

Re: [Bioc-devel] Compiling a cpp source code while installing package

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 --

Re: [Bioc-devel] Would it make sense for BiocManager::install to cache downloaded packages?

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

Re: [Bioc-devel] Vignette building error in multiGSEA

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’

Re: [Bioc-devel] Regarding installation of bioconductor version 2.13

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

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

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

[Bioc-devel] Fwd: Orchid ID invalid according to BiocCheck

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

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

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

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

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. <

[Bioc-devel] Project-wide code of conduct for Bioconductor

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

Re: [Bioc-devel] MPFE Bioconductor package

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

Re: [Bioc-devel] Best object structure for representing a pairwise genome alignment ?

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

Re: [Bioc-devel] Question about org.Dr.eg.db package

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"

Re: [Bioc-devel] non-conformable arrays

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

Re: [Bioc-devel] non-conformable arrays

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

Re: [Bioc-devel] non-conformable arrays

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

Re: [Bioc-devel] Resource temporarily unavailable error with rtracklayer

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

Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

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

Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

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

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

Eye color")$SNPS) > eyersids > [1] "rs12913832" "rs7173419" "rs3002288" "rs12896399" "rs1408799" > [6] "rs12520016" "rs288139" "rs1667394" "rs4596632" "rs12203592" > [11

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

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: > > >

Re: [Bioc-devel] How I hide non-exported function from the manual

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’

Re: [Bioc-devel] How I hide non-exported function from the manual

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

Re: [Bioc-devel] LazyData in DESCRIPTION file

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

Re: [Bioc-devel] a day in the life of gwascat

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 > &

Re: [Bioc-devel] a day in the life of gwascat

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

Re: [Bioc-devel] a day in the life of gwascat

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: >

[Bioc-devel] a day in the life of gwascat

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,

Re: [Bioc-devel] LazyData in DESCRIPTION file

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

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

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 ..

Re: [Bioc-devel] news on tidybulk?

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

Re: [Bioc-devel] news on tidybulk?

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: > > ___ >

[Bioc-devel] proper way to define an S4 method for 'plot'

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

Re: [Bioc-devel] Class for differentially expressed genes?

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

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

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’

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

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

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

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 >

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

~~~ > > 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

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

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

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

. 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

Re: [Bioc-devel] Annotation for Lactuca sativa (Lettuce)

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 #

Re: [Bioc-devel] A query about fixing bugs via github

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

Re: [Bioc-devel] FW: Repetitive variables within multiple function

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 &

Re: [Bioc-devel] Repetitive variables within multiple function

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

Re: [Bioc-devel] peculiar warning in BiocOncoTK

. 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

[Bioc-devel] peculiar warning in BiocOncoTK

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

[Bioc-devel] bioctitle issue for Rmd

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

Re: [Bioc-devel] proposal for additional seqlevelsStyle

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

[Bioc-devel] proposal for additional seqlevelsStyle

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

Re: [Bioc-devel] RangedData objects deprecated

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

Re: [Bioc-devel] -fopenmp switch issue on mac

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:

[Bioc-devel] -fopenmp switch issue on mac

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:

Re: [Bioc-devel] ndexr fails on vignette build on windows

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:

Re: [Bioc-devel] ndexr fails on vignette build on windows

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. > > >

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

> 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 >&

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

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 &

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

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

Re: [Bioc-devel] Build error due to TensorFlow installation

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

Re: [Bioc-devel] BiocCheck error

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

Re: [Bioc-devel] Is magrittr "%>%" acceptable in bioc packages?

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)

Re: [Bioc-devel] [ext] Re: Vignettes for a data processing package

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

Re: [Bioc-devel] Build error - C stack usage is too close to the limit

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

Re: [Bioc-devel] BioC packages - profileplyr

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

Re: [Bioc-devel] Problems with MACPET package

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

Re: [Bioc-devel] Fwd: banocc problems reported in the Multiple platform build/check report for BioC 3.9

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)

Re: [Bioc-devel] normalize_names_replacement_value error with colnames<- on SummarizedExperiment

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

[Bioc-devel] normalize_names_replacement_value error with colnames<- on SummarizedExperiment

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

[Bioc-devel] new error with saved HDF5SummarizedExperiment

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: ->

Re: [Bioc-devel] warnings with BiocStyle pdf compilation

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

[Bioc-devel] warnings with BiocStyle pdf compilation

*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

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

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

Re: [Bioc-devel] Help with installing netReg

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

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

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

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

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

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

The error on linux for 3.9: ## ## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RBGL ###

Re: [Bioc-devel] What is Bioconductor's position on allowing users to create files in the working directory without an explicit path definition in the filename

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

Re: [Bioc-devel] Question about package dependency

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

Re: [Bioc-devel] Questions about some checks in the latest BiocCheck

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

Re: [Bioc-devel] BioC 3.8 build Error

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

[Bioc-devel] a pattern to be avoided? mcols(x)$y <- z

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]>

Re: [Bioc-devel] Error: file larger than 5 Mb.

>> > 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

Re: [Bioc-devel] Error: file larger than 5 Mb.

(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

Re: [Bioc-devel] Question

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

Re: [Bioc-devel] Question about package development

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 #

Re: [Bioc-devel] Fwd: Vignette warnings/errors

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

Re: [Bioc-devel] Package download when using functions from affy and oligo

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

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

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

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

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

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

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

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

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%

Re: [Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

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

Re: [Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

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

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

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: >

Re: [Bioc-devel] "convert" graphics error for new submission

Maybe an antivirus issue? On Thu, Apr 5, 2018 at 8:30 PM, Vincent Carey <st...@channing.harvard.edu> wrote: > No, I did not do anything for this. > > On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >>

Re: [Bioc-devel] "convert" graphics error for new submission

No, I did not do anything for this. On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > It seems like this has 'gone away', was that something you did, or...? > > > > On 04/02/2018 04:34 PM, Vincent Carey wrote: > >> for two h

[Bioc-devel] "convert" graphics error for new submission

for two host-types I am seeing an error that I do not know how to address Loading required package: ontologyIndex sh: line 1: 76907 Abort trap: 6 'convert' 'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim 'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null sh: line 1: 76914 Abort

Re: [Bioc-devel] Error: node stack overflow

I get the following on MacOSX, after library(rJava); library(GenomicRanges) -- take rJava out of the mix and there is no error. I ran into this originally as an interaction between rJava and Gviz, and have reported to Florian. That seemed to be MacOSX-specific. > gr1 <-

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