Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

Hi Dario, The function was optimized in Bioc-devel. Depending on the number of records in your BAM file (which is more relevant than its size), it should now be between 2x and 5x faster. Please give it a try and let us know. Also keep in mind that the pairing algo will slow down if the average

Re: [Bioc-devel] Changing a name of a package already under review

One way to do this is to rename your GitHub repo and package, then to submit the new package as a new submission, and finally to close the original submission. Talk with your reviewer about this. S/he needs to know why you're closing the issue and where to find the new issue so s/he can follow

Re: [Bioc-devel] RnBeads 2.0

Hi Fabian, We'll take care of bumping all package versions (assumed to be in x.y.z format) to the next even y for the release (and reset z to 0). Packages with a x.99.z version will be treated specially: we'll bump x to x+1 and will reset y and z to 0. Right now RnBeads is at version 1.13.4

[Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

Hi developers, Starting with R 3.6, base::lengths() can now be treated as an S4 generic function (like base::length() or base::names()) so there is no need for us to define our own lengths() generic function in BiocGenerics. Therefore we've removed the lengths() generic from BiocGenerics (in

Re: [Bioc-devel] GenomicFeatures

FYI I've temporarily disabled the makeTxDbFromBiomart() examples in GenomicFeatures that have been responsible for this 'R CMD check' TIMEOUT for 2-3 days in a row: https://bioconductor.org/checkResults/3.8/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html Hopefully GenomicFeatures will pass

Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

Just to clarify we see these warnings on Mac only: https://bioconductor.org/checkResults/3.9/bioc-LATEST/NormalyzerDE/merida2-checksrc.html https://bioconductor.org/checkResults/3.9/bioc-LATEST/M3C/merida2-checksrc.html They seem to indicate problems with CRAN packages xts, ggplot2, and ape.

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

Hi Vince, It looks like Michael took care of this in devel (thanks Michael):   https://github.com/Bioconductor/GenomicRanges/issues/11 H. On 10/3/18 08:20, Hervé Pagès wrote: > Hi Vince, > > This issue was reported here a couple of weeks ago: > >

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

Hi Kylie, I've modified coerce2() in S4Vectors 0.21.5 so that `coerce2(from, to)` should now do the right thing when 'to' is a DataFrame derivative: https://github.com/Bioconductor/S4Vectors/commit/48e11dd2c8d474c63e09a69ee7d2d2ec35d7307a With the following gotcha: this will work only if

Re: [Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)

Hi guys, OTOH indexMTGenome() only takes 20s on my laptop to create, install and load GmapGenome.Hsapiens.rCRS. Note that the size on disk of GmapGenome.Hsapiens.rCRS is 449M which is surprising considering that the input of indexMTGenome() is a tiny 83K FASTA file. That's for the source

Re: [Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

uFKgRjCs=>> From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Pages, Herve mailto:hpa...@fredhutch.org>> Sent: Friday, November 2, 2018 6:08:13 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject:

Re: [Bioc-devel] BioC 3.9 devel builds

Hi Michael, I don't think we have any package that require C++14 at the moment. I see 36 software packages that have SystemRequirements: C++11 in devel. I agree that package authors should probably stick to that and avoid C++14 for now. The change I made to the build system is just a minor

Re: [Bioc-devel] Controlling vignette compilation order

Hi Aaron, Right now 'R CMD build' evaluates all vignettes in the same R session. Personally I see this as an undesirable feature and hope that it will change in the future. Problem with this is that when a vignette hits the max DLL limit, breaking it down into smaller vignettes doesn't help.

Re: [Bioc-devel] GenomicFeatures export request

Hi Leo, This is done in GenomicFeatures 1.35.4: https://github.com/Bioconductor/GenomicFeatures/commit/0b596c18b69f55d097aff0c6cdbbfc0b2993c4aa Cheers, H. On 11/15/18 09:25, Leonardo Collado Torres wrote: > Hi Hervé, > > Looking into the details of GenomicFeatures::exonicParts() I see that >

Re: [Bioc-devel] V8 and ggraph

Hi Alper, As you can see here   https://cran.r-project.org/web/packages/V8/ and here   https://cran.r-project.org/web/packages/ggraph/ CRAN doesn't provide OS X binaries of V8 and ggraph for r-devel yet so our build system is unable to install these packages. Whether this is going to be

Re: [Bioc-devel] Controlling vignette compilation order

This changes the default for _R_CHECK_BUILD_VIGNETTES_SEPARATELY_ from false to true so only affects the re-built of the vignettes during 'R CMD check'. While this is a step in the right direction, it would be good if  'R CMD build' was modified accordingly i.e. to also build vignettes in

Re: [Bioc-devel] Vignette Latex error

Hi Karl, On 4/2/19 15:03, Karl Stamm wrote: > I'm having a build error on only the OSX servers. > > * creating vignettes ... ERROR > --- re-building ‘rgsepd.Rnw’ using knitr > Error: processing vignette 'rgsepd.Rnw' failed with diagnostics: > Running 'texi2dvi' on 'rgsepd.tex' failed. > LaTeX

Re: [Bioc-devel] Pushing towards a better home for matrix generics

en do we >> think the aliases would be break? >> >> Andrew McDavid >> Biostatistics and Computational Biology >> Office: SRB 4.206 Ph: 585.275.5983 >> >> Message: 1 >> Date: Sun, 10 Feb 2019 13:36:43 + >> From: Aaron Lun >> mailto:infinite.

Re: [Bioc-devel] "vdiffr" package load fail on celaya2

Hi Jurrian, Many Mac binary packages for R 3.6 are still not available on CRAN. gdtools (which CHETAH indirectly depends on, via the vdiffr package) is one of them: https://cran.r-project.org/package=gdtools Other Bioconductor packages that fail because they depend (directly or indirectly)

[Bioc-devel] pandoc on celaya2

Hi package developers, 3 Bioconductor packages (ClusterJudge, KinSwingR, and YAPSA) are currently failing to build on celaya2 because of a pandoc-citeproc error that looks like: Error parsing references: Could not read as Int: "October" See:

Re: [Bioc-devel] Can I use .Rbuildignore to ignore .BBSoptions?

Hi Gordon, My understanding is that adding .BBSoptions to the .Rbuildignore file will tell 'R CMD build' to not include the file in the resulting source tarball, which is good (cleaner tarball). And since the build system reads the .BBSoptions file from the package source tree, not from the

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

Hi Koustav, From a Build System point of view, we certainly don't want packages to write files to the user's home (or to the current directory, which might be different from the user's home) during 'R CMD build' and 'R CMD check'. (Note that there is actually no guarantee that the current

Re: [Bioc-devel] build/check reports and package version available for updated package

Hi Ramon, We run the software builds every night and normally the build report gets updated every morning (for the people on the East Coast). However sometimes things don't work as expected. This time the builds went fine but the script that updates the report failed so that's why we still see

Re: [Bioc-devel] Pushing towards a better home for matrix generics

sion can be avoided by specifying signature="x" in the definition of the implicit generic. It formalizes where dispatch really happens and sets expectations upfront. No loose ends. Hope this makes sense, H. On 1/29/19 09:43, Martin Maechler wrote: >>>>>> Pages, Herve >>

Re: [Bioc-devel] Pushing towards a better home for matrix generics

ill need to change. Not sure how > > many packages will need to be fixed outside of Matrix, but > > it's not an isolated change. Martin might comment on the > > rationale for the full signature, since he defined those > > generics. > > > On Mo

Re: [Bioc-devel] missing devel experiment data builds

Thanks Charlotte for bringing this to our attention. Yes it looks like there are some serious issues with the data experiment builds. Sorry for that. We're working on it and will try to have them back on their feet for the next build iteration (experiment data builds are scheduled to run on

Re: [Bioc-devel] Pushing towards a better home for matrix generics

for this? H. On 1/28/19 19:00, Michael Lawrence wrote: > I agree (2) is a good compromise. CC'ing Martin for his perspective. > > Michael > > On Mon, Jan 28, 2019 at 6:58 PM Pages, Herve wrote: >> Hi Aaron, >> >> The 4 matrix summarization generics currently defin

Re: [Bioc-devel] Pushing towards a better home for matrix generics

Hi Aaron, The 4 matrix summarization generics currently defined in BiocGenerics are defined as followed:   setGeneric("rowSums", signature="x")   setGeneric("colSums", signature="x")   setGeneric("rowMeans", signature="x")   setGeneric("colMeans", signature="x") The only reason for having

Re: [Bioc-devel] Question: error in makeTxDbFromUCSC

Hi there, I answered this yesterday on the support site:   https://support.bioconductor.org/p/117265/#117346 Cheers, H. On 1/26/19 05:13, Vincent Carey wrote: > If I am not mistaken the same problem is on the support site and I provided > some > commentary at >

Re: [Bioc-devel] SetMethod to dispatch on class in unattached package

Hi Michael, So IIUC this upfront class registration wouldn't do much beside making the "no definition for class 'seurat'" message issued by setMethod disappear. Maybe that's not enough to justify adding more bloat to the methods package? My 2 cents, H. On 1/30/19 13:35, Michael Lawrence

Re: [Bioc-devel] missing devel experiment data builds

Hi Charlotte, The experiment data builds are back: https://bioconductor.org/checkResults/devel/data-experiment-LATEST/ Cheers, H. On 1/29/19 15:14, Pages, Herve wrote: > Thanks Charlotte for bringing this to our attention. Yes it looks like > there are some serious issues with th

Re: [Bioc-devel] Vignette Latex error

with the natbib standard, and meanwhile did some reformatting of the vignette overall. On Thu, Apr 4, 2019 at 7:47 PM Pages, Herve mailto:hpa...@fredhutch.org>> wrote: Hi Karl, On 4/2/19 15:03, Karl Stamm wrote: > I'm having a build error on only the OSX servers. > > * creating vign

[Bioc-devel] Packages with broken unit tests because of sample() change in R 3.6

Dear developers, As reported on this list in March (https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html) the sample() function has changed in recent R-devel. This change breaks the 19 following Bioconductor software packages: - cicero - clipper - clusterExperiment - CMA

[Bioc-devel] Packages with broken setClass statement

Dear developers, Here is another change in recent R devel that affects a few Bioconductor software packages. setClass() used to be tolerant to typos when specifying slot names in the prototype of the class. E.g. this works in R 3.5: setClass("A", slots=c(stuff="ANY"),

Re: [Bioc-devel] Pushing towards a better home for matrix generics

:57 AM Michael Lawrence mailto:micha...@gene.com>> wrote: Not yet. Too busy breaking other things ;) I'll move it up on my TODO list. On Thu, Mar 28, 2019 at 9:16 AM Pages, Herve mailto:hpa...@fredhutch.org>> wrote: Hi Michael, Did you get a chance to make this change? Thanks, H.

Re: [Bioc-devel] New build report

Hi Alina, For some unknown reason tokay1 stopped building in the middle of the night so we have no results for Windows on the RELEASE_3_8 build report today. The cause of tokay1's failure is under investigation. Sorry for the inconvenience, H. On 4/15/19 09:23, Alina Selega wrote: > Hi, >

Re: [Bioc-devel] TIMEOUT and tokay2 require Rmpi

Hi, See https://github.com/Bioconductor/Contributions/issues/1087#issuecomment-483315908 for why the package has a timeout on malbec2. It's a snow/doSNOW/Rmpi problem. Cheers, H. On 4/14/19 22:53, 郝洁 wrote: Hi, Our package SINCE has got TIMEOUT notice several times, but it only took a few

Re: [Bioc-devel] Packages with broken unit tests because of sample() change in R 3.6

qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=8-j7ZmUPgzjbPjswR-NgkqVYXyuW5sLTrpbH8t-C-wk=cpkWykYsvaXUWf5hpSIUqpoRis480-xt46plnJiHVkk= > to resolve the issue with derfinderHelper. > > Best, > Leo > > On Mon, Apr 8, 2019 at 6:40 PM Pages, Herve wrote: >> Dear developers,

Re: [Bioc-devel] memory exhausted on tokay2

am wondering why it needs that much RAM on Windows/Linux. If you can give me some more hints I'd be glad. Cheers, Aaron Am So., 7. Apr. 2019 um 00:03 Uhr schrieb Pages, Herve mailto:hpa...@fredhutch.org>>: Hi Aaron, Maybe the particular example (plotting) where the "memory

Re: [Bioc-devel] New package submission failing only in devel due to dependent package errors

Hi Daniel, The 'invalid class "VCFHeader" object' error on Windows has been fixed in Rhtslib 1.15.6. Cheers, H. On 4/11/19 04:04, Daniel Cameron wrote: > The package adds structural variant functionality on top of > VariantAnnotation. It's been pretty stable for the last 18 months and >

Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package

Hi Erik, The 'invalid class "VCFHeader" object' error on Windows has been fixed in Rhtslib 1.15.6. Cheers, H. On 3/18/19 00:36, Erik Fasterius wrote: > Hi, Valerie! > > Thanks for looking into the problem! I hope it’ll work out. > > Erik > > On 16 Mar 2019, at 22:51, Valerie Obenchain >

Re: [Bioc-devel] GWASTools error on tokay related to VariantAnnotation::readVcf

Hi Stephanie, The 'invalid class "VCFHeader" object' error on Windows has been fixed in Rhtslib 1.15.6. Cheers, H. On 4/11/19 11:28, Shepherd, Lori wrote: > Please ignore this ERROR for now. It is a known issue in VariantAnnotation > and we are working on the patch. You can ignore this

Re: [Bioc-devel] deprecation guidelines

Hi Sam, On 4/11/19 10:47, Samuela Pollack wrote: > Dear Bioconductor, > > We are deprecating part of a package. I am following the guidelines in > the "Function Deprecation Guidelines" page at bioconductor.org and I > have a few questions: > > (i) Deprecating a S4 method which has the same name

Re: [Bioc-devel] SummarizedExperiments not equal after serialisation

Let's try to go to the bottom of this. But let's leave SummarizedExperiment objects out of the picture for now and focus on what happens with a very simple reference object. When you create 2 instances of a reference class with the same content: A <- setRefClass("A", fields=c(stuff="ANY"))

Re: [Bioc-devel] IRanges should support long vectors

Hi Pariksheet, On 5/25/19 12:49, Pariksheet Nanda wrote: Hello, R 3.0 added support for long vectors, but it's not yet possible to use them with IRanges. Without long vector support it's not possible to construct an IRanges object with more than 2^31 elements: ir <- IRanges(start = 1:(2^31

Re: [Bioc-devel] index of Bioc repository unavailable

Hi Laurent, This is temporary. We're in the process of creating the 3.10 annotation repo by "forking" the 3.9 annotation repo. As part of this process, we run a script that generates the PACKAGES index for the new 3.10 annotation repo. The process will take a few more hours before it completes.

Re: [Bioc-devel] IRanges should support long vectors

instance # seq: TCCTTGAAAAC We should probably have something like that in the BSgenome package. Also opened an issue for that one: https://github.com/Bioconductor/BSgenome/issues/3 Best, H. > > Pariksheet > > On Tue, May 28, 2019 at 3:35 AM Pages, Herve <mailto:hpa...@fr

Re: [Bioc-devel] get_dcf_info failed and build intervals

ion data set, read those in. > > Thanks, will do that before next push to master. > > Best S > > > On Fri, Jun 14, 2019 at 7:37 PM Pages, Herve <mailto:hpa...@fredhutch.org>> wrote: > > On 6/14/19 15:58, Shraddha Pai wrote: > > Hi, > &g

Re: [Bioc-devel] get_dcf_info failed and build intervals

Hi, From the Linux command line: git clone https://github.com/BaderLab/netDx R CMD INSTALL netDx * installing to library ‘/home/hpages/R/R-3.6.r76454/library’ Error: error reading file '/home/hpages/sandbox/netDx/DESCRIPTION' R CMD build netDx * checking for file

Re: [Bioc-devel] get_dcf_info failed and build intervals

le by putting in line > breaks in the "description" field, which caused the build to fail. My bad. > > Thank you for the feedback, I'm running the build on my machine to make > sure there are no more trivial errors. > > Regards > Shraddha > > On Fri, Jun 14,

Re: [Bioc-devel] new error with saved HDF5SummarizedExperiment

Hi Vince, This was just a temporary glitch introduced in devel by some recent changes to SummarizedExperiment. Should work again now. Make sure you have the latest SummarizedExperiment and HDF5Array (1.15.1 and 1.13.2, respectively). Cheers, H. On 6/7/19 13:08, Vincent Carey wrote: > Loading

Re: [Bioc-devel] error regarding splitAsList from IRanges packages

Hi Felix, Another temporary glitch introduced in devel by some recent changes to S4Vectors/IRanges, sorry. I think I fixed all the affected packages (was going to fix RNAmodR too but you beat me to it ;-) ). No more splitAsList related issues on today's build report :-) Cheers, H. On 6/7/19

Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi Jianhong, We found that another software package has code in its examples that is reinstalling org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg18, and TxDb.Hsapiens.UCSC.hg18.knownGene. This causes problems in the context of the nightly builds were many packages are checked simultaneously. After a

Re: [Bioc-devel] No such file or directory: BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit

Hi Paul, After a long hunt, the software package causing these daily reinstallations of BSgenome.Hsapiens.UCSC.hg38 has been identified and his maintainer contacted. Sorry for the inconvenience this has caused so far. H. On 6/24/19 12:31, Paul Shannon wrote: > Warning in

Re: [Bioc-devel] SBGNview package build error: data package not available. (SBGNview.data not in build/check results)

Also please note that data experiment packages are on a different report (and SBGNview.data is in it): https://bioconductor.org/checkResults/3.10/data-experiment-LATEST/ As Lori said it can take a few build cycles before SBGNview.data gets installed on all the build machines. H. On 6/25/19

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

On 6/12/19 08:26, Vincent Carey wrote: > remedied by installation of latest S4Vectors/SummarizedExperiment from git Good. I just fixed this in git/github 5 min ago: https://github.com/Bioconductor/SummarizedExperiment/commit/01aa07a87b72b7423bea38028fffba4e896fdcf3 H. > > On Wed, Jun 12,

Re: [Bioc-devel] package that will not build under Windows with Rtools35 (but works with Rtools40)

Hi Ramon, We try to not be adventurous with what we put on the build machines so we'd like to stick to whatever Rtools version is officially the current stable one. Also we don't have a mechanism for switching to a different package code base or branch on some platforms. This wouldn't be a good

Re: [Bioc-devel] Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled

Hi Nitesh, I'm running into some problems today when trying to push a commit to BiocGenerics: hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$ git remote -v origin

Re: [Bioc-devel] Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled

to avoid these false positives. Thanks, H. On 5/11/19 13:37, Pages, Herve wrote: Hi Nitesh, I'm running into some problems today when trying to push a commit to BiocGenerics: hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/soft

Re: [Bioc-devel] loading database package changes random number

er stream in BiocParallel for what amounts to a pretty trivial and probably dubious strategy [choosing random ports in hopes that one is not in use], but that starts to sound like a more substantial feature. Martin On 4/11/19, 7:06 PM, "Pages, Herve" <mailto:hpa...@fredhutch.org&

Re: [Bioc-devel] When to use generics?

Hi Boris, AFAICT the ::() syntax also works well with generics. Note that people sometimes specify the that exports some specific method for the generic when they should actually specify the where the generic is defined. One thing about the "regular function with if (is()) statements" vs

Re: [Bioc-devel] readVcf problems in package check

Hi Lindsay, Is this issue specific to the Windows CRAN checks? This Windows-specific error was also affecting several Bioconductor packages until recently but has been addressed in the latest version of Rhtslib (v 1.15.6). What version of Rhtslib are they using for the CRAN checks? They need

Re: [Bioc-devel] package size issue

Interesting observation Boris. The software packages currently have 1261 pdf vignettes and 983 html vignettes in BioC 3.9. Here are some quick stats that confirm Boris' observation (sizes are in bytes): > summary(pdf.sizes)     Min.  1st Qu.   Median Mean  3rd Qu. Max.     5267  

Re: [Bioc-devel] builds of last 2 days

Hi Karim, Today's report has not arrived yet. You bumped canceR's version to 1.18.3 on May 6 (i.e. yesterday): biocbuild@malbec2:~/canceR$ git show 77cab2a7 DESCRIPTION commit 77cab2a7f7995fdb3de348893d45bbb3a5f15f7c (HEAD -> RELEASE_3_9, origin/RELEASE_3_9) Author: kmezhoud Date:

Re: [Bioc-devel] R CMD check testthat failure in tokay2 (devel branch)

Hi Benjamin, Sorry for the late answer. Looks like things have changed a little bit on the report since your original post. What I see on today's report is a test failure on Windows for the i386 arch only:

Re: [Bioc-devel] How to change the name of R package that is already published on Bioconductor?

Hi Juanpeng, I notice that the new miRspongeR package also displays the package startup message explaining the name change from miRsponge to miRspongeR.. Note that you only need to have this message in the old miRsponge package (which is now officially deprecated in BioC 3.9). Having the

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

Hi Qiang, On 4/26/19 11:47, Hu, Qiang wrote: > Hi all, > > > Could you please help to check whether the required python package "cwltool" > is installed and works in malbec2 and celaya2? > > Here is part of the error log in malbec2: > > $cwltool --version > > ... > >

Re: [Bioc-devel] celaya2: Warning: multiple methods tables found for rowSums

Hi Ahmed, This warning is due to some stale methods tables on celaya2. It will go away and can safely be ignored. Cheers, H. On 4/19/19 16:32, Ahmed Youssef wrote: > Hi everyone, > > I am getting a strange warning only on celaya2 for my package: > Warning: multiple methods tables found for

[Bioc-devel] No build report today (April 24, 2019)

Hi developers, Due to some technical problems with the build system, there will be no new build report today for the BioC 3.10 software builds. Sorry for the inconvenience. H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research

Re: [Bioc-devel] No build report today (April 24, 2019)

On 4/24/19 10:48, Pages, Herve wrote: > Hi developers, > > Due to some technical problems with the build system, there will be no > new build report today for the BioC 3.10 software builds. I meant for the BioC 3.9 builds sorry. (There won't be a report for the BioC 3.10 b

Re: [Bioc-devel] Unable to reproduce chimeraviz 3.9 build failure (test failure)

Hi Stian, This is likely related to an issue with the recently updated org.Hs.eg.db package. The issue was reported on this list 2 days ago: https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014956.html A fix for org.Hs.eg.db is on its way. Hopefully it will make the current test failure

Re: [Bioc-devel] "vdiffr" package load fail on celaya2

ZvSXAJJKaaPhzWA=2y3uBzesEzjNWMJIdx58GP6F6XQRp5SWkF_1byBDAPU=xogs34MyCr0KUp8B3rB2tCDwjgcwIq6Lts11ATQPMIk=> On Sun, Apr 7, 2019 at 10:34 PM Pages, Herve mailto:hpa...@fredhutch.org>> wrote: Hi Jurrian, Many Mac binary packages for R 3.6 are still not available on CRAN. gdtools (which CHETAH indirectly de

Re: [Bioc-devel] package rJava can not be loaded in build system OS X

Hi Zheng, We're working on this and will provide an update ASAP. Note that this won't affect the release of the esATAC Mac binary, which is already available in BioC 3.9 (see at the bottom of the landing page): https://bioconductor.org/packages/3.9/bioc/html/esATAC.html This is because it

Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

me. There is no parallelization in this class - but maybe the > build system introduces some at a higher level? > > I can condition these failing tests on hostname in order to pass the build > tests if that is not too much of a dodge. > > - Paul > > >> On Apr 23, 2019, at

Re: [Bioc-devel] package rJava can not be loaded in build system OS X

The problem has been addressed. However, the fix came after the nightly builds started today so some packages will still be affected on tomorrow's report. The problem should clear out completely after tomorrow. Cheers, H. On 4/25/19 15:03, Pages, Herve wrote: > Hi Zheng, > > We'r

Re: [Bioc-devel] loading database package changes random number

Hi Steffi, Any code that gets called between your calls to set.seed() and runif() could potentially use the random number generator. So the sequence set.seed(123); runif(1) is only guaranteed to be deterministic if no other code is called in between, or if the code called in between does not

Re: [Bioc-devel] Release push DENIED by fallthru (REMP)

Hi Yinan, The RELEASE_3_8 branch was frozen 8 days ago. This was announced on this list: https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014931.html Best, H. On 4/23/19 13:53, Yinan Zheng wrote: > Hi Bioc Devel Team, > > I fixed some bugs in my package REMP but failed to push the

Re: [Bioc-devel] memory exhausted on tokay2

check/pkg-Ex.R", echo = TRUE, max = Inf) Martin On 4/17/19, 5:31 AM, "Bioc-devel on behalf of Pages, Herve" mailto:bioc-devel-boun...@r-project.org> on behalf of hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>> wrote: Hi Aaron, I used 'top' on merida1 (on

Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

Hi Paul, Is there a possibility that trena's code is having one worker downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same time another worker is trying to access it? The reason I suspect something like this is that it seems that BSgenome.Hsapiens.UCSC.hg38 gets

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

Hi Aaron, On 4/25/19 16:44, Aaron Lun wrote: It doesn't seem like it - on my installation, org.Hs.eg.db is still... monkeying around. __ w c(..)o ( \__(-)__) /\ ( /(_)___) w /| | \ m m Daniel has prepared a new

Re: [Bioc-devel] erro in package build

Hi Claudio, As you can see on our build/check report, what is broken is 'R CMD INSTALL Mulcom'. The problem is easy to reproduce: hpages@spectre:~$ git clone https://git.bioconductor.org/packages/MulcomCloning into 'Mulcom'... remote: Enumerating objects: 570, done. remote: Counting

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

This is a really important point. Finding and updating serialized S4 instances that are lying around as they evolve can be painful and very time-consuming. We should definitely avoid storing serialized S4 objects on the Hub. I don't know about ExperimentHub but at least for AnnotationHub I

Re: [Bioc-devel] Resetting to previous commits

On 8/14/19 10:19, Kasper Daniel Hansen wrote: ... > > Pro-tip: In general, you will be well served not to get too attached to > version numbers. Bump it frequently even without new functionality or bug > fixes and just live with the frequent bumping. +1 for Best Advice Of The Week. -- Hervé

Re: [Bioc-devel] BiocCheck error

Note that the name of the package (BioTIP) differs from the name of the GitHub repo (NPS). They will need to match if you intend to submit to Bioconductor. Thanks! H. On 8/20/19 09:20, Zhezhen Wang wrote: > I see, thank you Martin! > Zhezhen > > From: Martin

Re: [Bioc-devel] BiocCheck error

. > > Zhezhen > -------- > *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-d

[Bioc-devel] Changes to DataFrame

Hi developers, Short story: these changes shouldn't affect you but I recommend you read the long story just in case. Long story: Some of you maybe already noticed that I was making changes to the DataFrame class. The idea is to "make room" for other data-frame-like containers by having

Re: [Bioc-devel] Whether to copy unexported BSgenome function into multicrispr

Hi Aditya, I've added the 'load.only' argument to getBSgenome(). This is in BSgenome 1.53.2. See https://github.com/Bioconductor/BSgenome/commit/0eeddb5c0f57c69a0db31874b7b031ba06720bee This change will propagate to BioC devel in the next couple of days. Cheers, H. On 8/28/19 02:18, Bhagwat,

Re: [Bioc-devel] Error: DLL 'rgl' not found: maybe not installed for this architecture?

Hi, On 8/23/19 14:38, Venu Thatikonda wrote: > Hi, > > During one of my R packages bioc review, I see the following 2 errors, > > one: > > Error in library.dynam(dynlib, pkg, lib) : >DLL 'rgl' not found: maybe not installed for this architecture? > Error: .onLoad failed in loadNamespace()

Re: [Bioc-devel] Samtools dependency

Hi Jonathon, Have you considered depending on Rhtslib? See https://bioconductor.org/packages/Rhtslib Rsamtools itself is implemented on top of Rhtslib. Note that other Bioconductor packages (e.g. DiffBind, deepSNV, BitSeq, qrqc, QuasR, seqbias, TransView, etc...) use Rhtslib internally to

Re: [Bioc-devel] BiocCheck error

bW0WYiZvSXAJJKaaPhzWA=dujEzslWeMIvlTaSOpEXKPSBhHSgfjJdT-5vXztzjNc=o36ekG8m2LTVHqFWfa1uu-vxfFxjblw1UE8I7Nm5fpc= >> >> Obviously not ideal, and really a workaround for limitations on the >> Bioconductor side of the fence, but it would not result in two permanent >> github repositor

Re: [Bioc-devel] TENxBUSData not added to the Bioconductor git repository

Hi Lambda, Yes TENxBUSData was accepted but we only build data-experiment packages on Sundays, Tuesdays, and Thursdays so you might need to wait a couple extra days before you see TENxBUSData show up on the website and become available via BiocManager::install(). Thanks for your patience, H.

Re: [Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

Hi Marcel, Charles, Looks like S4Vectors:::coerceToSimpleList() is being to zealous here. I've tweaked the function a little (in S4Vectors 0.23.21) so that elements in the supplied list get coerced only when the 2nd argument (element.type) is specified. This fixes both Marcel's and Charles'

Re: [Bioc-devel] 'tokay1' error but passed other OS

Also note that since the error is specific to 32-bit Windows, you need to run 'R CMD check --force-multiarch' on your package source tarball in order to reproduce the error. Without the --force-multiarch flag, 'R CMD check' only runs the examples and unit tests for the default arch, which, for

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

Hi Simon, On 9/3/19 09:11, Simon Dirmeier wrote: ... Do you think it would be possible to install TensorFlow and TensorFlow-Probability on the builders? I'd assume that many would profit from that. As Lori mentioned at the end of her email (see below), we can't make the tensorflow Python

Re: [Bioc-devel] 'tokay1' error but passed other OS

On 9/4/19 14:10, Venu Thatikonda wrote: > @Lori, sure. I will open the issue with an example. > > @Daniel, I didn't understand, I thought this suggestion is for Lori (?). > > Do I need to run `R CMD check --force-multiarch` on a windows 32bit system > from my side? If that's the case, It won't

Re: [Bioc-devel] new package for accessing some chemical and biological databases

Hi, On 9/13/19 06:38, Morgan, Martin wrote: > 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

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

Hi Paul, On 9/12/19 11:47, Paul Shannon wrote: > My package igvR requires a web browser. Unit tests, examples, vignette all > will all fail if one is not available. > > Since the bioc build system, for good reason, does not provide a web browser, > I’d like to condition all browser-related

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Afqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY=nBHdQoTrd1Mfu4VTMgtkPyUQ0Ju2NLeX-0X1Ny3fSeg=>) > > Cheers, > > Aditya > > > > > > From: Pages, Herve [hpa...@fredhutch

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

On 9/11/19 00:50, Vincent Carey wrote: > 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 = " ")) : >

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Hi Aditya, It feels that a coercion method from BSgenome to GRanges should rather be defined in the BSgenome package itself. Patch/PR welcome on GitHub. More generally speaking, coercion methods should be defined in a place that is "as close as possible" to the "from" or "to" classes rather

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, On 9/16/19 06:35, Tiago Lubiana Alves wrote: > Hello Mike, > > Thank you for the detailed explanation. > > You are right, for the vignette, I can download it from the ExperimentHub > subset the pbmc3k dataset in the first few lines. The main point of having > a new dataset was to use

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