Re: [Bioc-devel] Build error in nebbiolo1 for package BgeeCall

Buffalo, New York 14263 From: Bioc-devel on behalf of Julien Wollbrett Sent: Monday, August 5, 2024 7:45 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error in nebbiolo1 for package BgeeCall Hello, I am the maintainer of the BgeeCall package.

[Bioc-devel] Build error in nebbiolo1 for package BgeeCall

Hello, I am the maintainer of the BgeeCall package. There is an issue in the build of the package on nebbiolo1 since at least the last Bioconductor release. The error comes from the vignette when I try to load data from the AnnotationHub package. I am not able to reproduce the error locally. Do

Re: [Bioc-devel] Build Error for ANCOMBC Package on Linux

Hi Huang, That's because the latest version of CVXR (1.0-14, uploaded to CRAN on June 27) introduces a dep on the new clarabel package (also on CRAN since June 22): https://cran.r-project.org/package=clarabel Unfortunately clarabel has a bunch of system requirements that are not on our Linux

[Bioc-devel] Build Error for ANCOMBC Package on Linux

Dear BioC Team, I am the maintainer of the ANCOMBC package http://bioconductor.org/packages/release/bioc/html/ANCOMBC.html I recently received messages from the system indicating that ANCOMBC encountered a build error on the Linux system. The error message is as follows: ``` * installing to

Re: [Bioc-devel] Build error on nebbiolo2

Hi Gregory, Looks like GDAL is missing on nebbolo2. We're looking into this. Thanks for letting us know, H. On 10/23/23 10:25, Gregory B. Gloor wrote: > Hello, > > I received an error today on this machine for ALDEx2 > > I last committed 12 days ago and until today it was building cleanly on

[Bioc-devel] Build error on nebbiolo2

Hello, I received an error today on this machine for ALDEx2 I last committed 12 days ago and until today it was building cleanly on everything. I am not sure what I can do to fix the error since I don't know what dependency is calling that library file Any help appreciated Greg

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Martin, Agreed that FMA [1] could be the cause. Anyhow, I had disabled that specific unit-test. That is the quickest fix right now to meet the Bioconductor 3.18 release date. I will try to revisit the C code that you mentioned and see if I can fix the problem. Thanks so much for your help!

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Reina, I tried to debug it but without success! I think the problem is at https://code.bioconductor.org/browse/CaDrA/blob/devel/src/score_fun.c#L613 because it fails only with method = "ks_score" It does a lot of calculations with doubles and I am almost sure FMA [1] is to blame. You could try

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Martin, Yes, I removed that specified test case that failed the check in order to meet Bioconductor 3.18 release deadline. Thanks again for looking into this! Best, Reina C. On Oct 19, 2023, at 4:20 AM, Martin Grigorov wrote: Hello Reina, The checks pass now after your last commit:

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hello Reina, The checks pass now after your last commit: ``` ... * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Martin, That would be very helpful. Thanks so much! Right now, it is failing in one of the unit test cases. In particular, our core function, CaDrA::CaDrA, which is used to run permutation-based tests to determine whether the strength of the association between the set of features and the

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina wrote: > Thank you both! I will look thru the links and see if I can implement a > fix. > I'd be happy to test any patches if it will be easier for you ! Martin > > Best, > > Reina C. > > On Oct 18, 2023, at 4:03 PM, Martin Grigorov > wrote: > >

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Thank you both! I will look thru the links and see if I can implement a fix. Best, Reina C. On Oct 18, 2023, at 4:03 PM, Martin Grigorov wrote: Hi, On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès mailto:hpages.on.git...@gmail.com>> wrote: Hi Reina, Note that CaDrA results on Mac ARM64 are

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi, On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès wrote: > Hi Reina, > > Note that CaDrA results on Mac ARM64 are also affected: > https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/ > > See Martin Grigorov's blog post here >

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Reina, Note that CaDrA results on Mac ARM64 are also affected: https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/ See Martin Grigorov's blog post here https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/ for how to debug Linux ARM64 related

[Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi Bioconductor Core Team, I’m the maintainer of CaDrA package, and recently, I notice that my package built successfully for all platforms except on Kunpeng2 Linux machine (see https://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/ and

Re: [Bioc-devel] Build error - Latex environment in vignettes

From: Bioc-devel on behalf of Sergio Picart Armada Sent: Sunday, February 26, 2023 3:38 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error - Latex environment in vignettes ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown

[Bioc-devel] Build error - Latex environment in vignettes

Dear bioc-devel list, I am the maintainer of the FELLA package. I got some BUILD errors related to the LaTeX environments: Release: error only on lconway * creating vignettes ... ERROR --- re-building

Re: [Bioc-devel] Build error accessing cache of ExperimentHub on windows platform

The error seems to be fixed now :) This just happened in one of the reports, unsure what was the error. From: Dolors Pelegrí Date: Wednesday, 26 October 2022 at 14:54 To: "Kern, Lori" Cc: "bioc-devel@r-project.org" , "Lapuente Santana, Oscar" Subject: Re: [Bio

Re: [Bioc-devel] Build error accessing cache of ExperimentHub on windows platform

; Sent: Wednesday, October 26, 2022 5:39 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Build error accessing cache of ExperimentHub on > windows platform > > Dear Bioconductor developers/maintainers, > > A build error related to accessing the cache of ExperimentHub o

Re: [Bioc-devel] Build error accessing cache of ExperimentHub on windows platform

5:39 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error accessing cache of ExperimentHub on windows platform Dear Bioconductor developers/maintainers, A build error related to accessing the cache of ExperimentHub occurred just in windows platform (my package depends on �ea

[Bioc-devel] Build error accessing cache of ExperimentHub on windows platform

Dear Bioconductor developers/maintainers, A build error related to accessing the cache of ExperimentHub occurred just in windows platform (my package depends on ‘easierData’ package which contains ExperimentHub objects). My package ‘easier’ used was installing, building and checking correctly

Re: [Bioc-devel] Build error

Thanks for your note. I had a look at your vignette and found devtools::install_github('christophergandrud/repmis') That's not permitted. repmis is on CRAN and seems synced with the github repo, so please take this out. You also have a download event in the vignette. > source_data("

[Bioc-devel] Build error

Hi - The PoTRA package has not experienced build errors for the majority of the last two years until recently. Can you clarify if these build errors are due to bioconductor environmental failure or hardware failure? If not, can you help me understand the build error root cause so that I can

Re: [Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible

Bengtsson Sent: Donnerstag, 17. Juni 2021 17:21 To: bodenho...@bioinf.jku.at Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible On Thu, Jun 17, 2021 at 2:32 AM wrote: > > Dear colleagues, >

Re: [Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible

On Thu, Jun 17, 2021 at 2:32 AM wrote: > > Dear colleagues, > > It seems to me that, starting with the latest BioC devel branch (3.14), the > build systems have become more pedantic about logical vectors of length > 1 > in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil' >

[Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible

Dear colleagues, It seems to me that, starting with the latest BioC devel branch (3.14), the build systems have become more pedantic about logical vectors of length > 1 in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil' currently fail to build. Surely I want to fix this.

Re: [Bioc-devel] Build error on Mac re: Arial font and polygon edges

Good morning Hervé, Thank you - I checked Monday am, and sure enough those errors were resolved. Best,Shraddha On Fri, Apr 30, 2021 at 8:51 PM Hervé Pagès wrote: > Hi Shraddha, > > Hundreds of Bioconductor packages are affected since yesterday. Please > ignore. > > Today we've upgraded R to R

Re: [Bioc-devel] Build error on Mac re: Arial font and polygon edges

Hi Shraddha, Hundreds of Bioconductor packages are affected since yesterday. Please ignore. Today we've upgraded R to R 4.1 alpha on machv2, and made a tweak to the setup, so hopefully these errors will be gone on tomorrow's report. Best, H. On 4/30/21 2:46 PM, Shraddha Pai wrote: Hello

[Bioc-devel] Build error on Mac re: Arial font and polygon edges

Hello BioC community, My package netDx is building correctly on Linux but has the following issues on Mac: When running the vignette BuildPredictor.Rmd, 1) we get the error: Warning in doTryCatch(return(expr), name, parentenv, handler) : no font could be found for family "Arial" 2) the

[Bioc-devel] build error on EnMCB package

Hello BioConductor team, We have a build error problem. We tested our package locally and find that the function cph in cms packages has changed recently which caused the error. We changed the function and tested in our environment and submitted it to git.bioconductor.org, however the error

Re: [Bioc-devel] Build error for pwrEWAS

Hi Stefan, Pasting the reply from Mike Smith, a few hours ago, in the email thread "Error in building vignette for previously stable version": This looks like the same problem a few others have reported. The latest > advice was to wait for BiocStyle to be updated to reflect changes in >

[Bioc-devel] Build error for pwrEWAS

Dear bioc-devel team, I have received a notification that the build of my package (without any changes) resulted in the following error. I would appreciate some assistance, because I don't know what is causing the error. Thanks, Stefan ! LaTeX Error: Command \VerbBar already defined.

Re: [Bioc-devel] Build error

Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Kumar, Ashwath Sent: Wednesday, December 4, 2019 11:10 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build erro

[Bioc-devel] Build error

Hello bioc-devel team, I recently came across an error when the automatic bot was trying to build my package. The error only happens on OSX systems. === R CMD BUILD === * checking for file CSSQ/DESCRIPTION ... OK * preparing CSSQ: *

Re: [Bioc-devel] Build error upon bioc-issue-bot check

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Raphael Bonnet Sent: Tuesday, October 8, 2019 11:56 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error upon bioc-issue-bot check Hi, I just had c

[Bioc-devel] Build error upon bioc-issue-bot check

Hi, I just had committed a new verison of my package in issue #1282, when bots started to report "skipped, ERROR" for every hosts. Build report show * * *PostProcessing*:Accessing git_info complete. Accessing git_info complete. Git clone Failed. Git clone Failed. On my side git clone works

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

t;>> windows error can be ignored for now. > >>> > >>> > >>> > >>> Lori Shepherd > >>> > >>> Bioconductor Core Team > >>> > >>> Roswell Park Cancer Institute > >>> > >>> Depa

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

Simon Dirmeier <mailto:simon.dirme...@web.de> *Sent:* Monday, September 2, 2019 6:08:45 AM *To:* bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <mailto:bioc-devel@r-project.org> *Subject:* [Bioc-devel] Build error due to TensorFlow installation Dear all, since I replaced some o

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

statistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > *From:* Bioc-devel on behalf of > Simon Dirmeier > *Sent:* Monday, September 2, 2019 6:08:45 AM > *To:* bioc-devel@r-project.org

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

oc-devel on behalf of Simon Dirmeier Sent: Monday, September 2, 2019 6:08:45 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error due to TensorFlow installation Dear all, since I replaced some old C++ code with TensorFlow I am getting some build errors on merida1 and tokay1 r

[Bioc-devel] Build error due to TensorFlow installation

Dear all, since I replaced some old C++ code with TensorFlow I am getting some build errors on merida1 and tokay1 regarding installation (even though I install TF and TF Probability during /.onLoad/) http://bioconductor.org/checkResults/devel/bioc-LATEST/netReg/merida1-buildsrc.html Does anyone

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

> I can confirm this. Would it then be appropriate for scMerge to add a > (>= 1.7.3) after its Imports: entry for SingleCellExperiment? I don't think this is really necessary; 1.7.3 will propagate soon enough, at which point people just need to stay updated. > Basically, before we commit

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] 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] Build error - C stack usage is too close to the limit

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 installing drisso/SingleCellExperiment off GitHub. The other moral of the story is to not use

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

Hi all, I am getting a strange build error message for scMerge (http://bioconductor.org/checkResults/devel/bioc-LATEST/scMerge/malbec1-buildsrc.html) that reads + "C stack usage is too close to the limit” on Linux and Mac and + "evaluation nested too deeply: infinite recursion” on Windows,

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

On 07/09/2018 11:00 AM, Sergio Picart Armada wrote: Thank you Morgan, I already fixed this by skipping the offending test on win32. I fixed the devel version, but the release version has not noticed the version bump (from 1.0.0 to 1.0.1). Did I forget anything? builds are nightly, not on

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

Thank you Morgan,  I already fixed this by skipping the offending test on win32.  I fixed the devel version, but the release version has not noticed the version bump (from 1.0.0 to 1.0.1).  Did I forget anything? Thank you again,  On Monday, May 21, 2018 18:58 CEST, Hervé Pagès wrote:  On

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

On 05/21/2018 05:50 AM, Martin Morgan wrote: Remember that 32-bit Windows can only address vectors that are less than 2^32 - 1 elements long -- it looks like your example is trying to do more than this, and the solution is to implement a more modest example. 32-bit Windows limits the amount

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

Remember that 32-bit Windows can only address vectors that are less than 2^32 - 1 elements long -- it looks like your example is trying to do more than this, and the solution is to implement a more modest example. Martin On 05/18/2018 04:05 AM, Sergio Picart Armada wrote: Dear Bioconductor

[Bioc-devel] Build error in tokay2: cannot reserve space for vector

Dear Bioconductor team,  I'm the maintainer of the FELLA package.  Lately the check in tokay2 has failed, see http://bioconductor.org/checkResults/release/bioc-LATEST/FELLA/tokay2-checksrc.html Specifically: Message: At vector.pmt:442 : cannot reserve space for vector, Out of memory Class:

Re: [Bioc-devel] Build Error processing vignette

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kucukural, Alper <alper.kucuku...@umassmed.edu> Sent: Friday, April 27, 2018 1:26:37 PM To: bioc-devel@r-project.org Subject

[Bioc-devel] Build Error processing vignette

Hi, I got build error processing the vignette. The error is Error: processing vignette 'DEBrowser.Rmd' failed with diagnostics: 'html_document2' is defunct. How can I solve this problem? Thanks, Alper Kucukural, PhD Assistant Professor, Program in Molecular Medicine Bioinformatics Core

Re: [Bioc-devel] Build error on windows (devel)

On Windows and Mac, we install binary versions of CRAN packages from CRAN, rather than building them from source; this is what users would do. For unknown reasons, the CRAN packages for R-devel (hence Bioc-devel, where your package is not building) are built against R-3.4.2, and are not

[Bioc-devel] Build error on windows (devel)

I’m getting an error on the Windows (tokay2) build for the devel version of my package for some reason. It looks like the error is because of an error in SummarizedExperiment, which is caused by an error in it’s dependencies. Any idea why this would happen?

Re: [Bioc-devel] build error on tokay1 related to Makeconf permission

Great, thanks for the update! -Alicia On Mon, Jun 12, 2017 at 6:14 AM Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Just closing the loop on this one. Permissions on the Windows Makeconf > were fixed - this error should not appear anymore. > > Valerie > > > On 05/24/2017 01:40

Re: [Bioc-devel] build error on tokay1 related to Makeconf permission

Just closing the loop on this one. Permissions on the Windows Makeconf were fixed - this error should not appear anymore. Valerie On 05/24/2017 01:40 PM, Alicia Schep wrote: > I have a question about a build error that I am seeing on tokay1 for a > submitted package (motifmatchr >

[Bioc-devel] build error on tokay1 related to Makeconf permission

I have a question about a build error that I am seeing on tokay1 for a submitted package (motifmatchr ): Warning in file(con, "r") : cannot open file 'C:/Users/BIOCBU~1/BBS-3~1.6-B/R/etc/x64/Makeconf': Permission denied Error in

Re: [Bioc-devel] Build error: "Could not fetch a url"

Hi Alper. I'm not sure what cache that would be. Could the problem be on the debrowser server side i.e. that the URL pointing to the PNG image hosted on the debrowser server sometimes cannot be fetched because the server is not accessible at that particular moment? Cheers, H. On 05/01/2017

[Bioc-devel] Build error: "Could not fetch a url"

Hi, I got this error in debrowser builds that I shouldn't get. Since, it builds without any problem most of the time but sometimes, I got this error below. Is it reading the links from the cache? How can I solve it? It works most of the time but sometimes I got this error like today.

Re: [Bioc-devel] Build error on tokay2

of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Alina Selega <alina.sel...@gmail.com> Sent: Tuesday, April 4, 2017 7:24:07 AM To: bioc-devel Subject

[Bioc-devel] Build error on tokay2

Hi, My package BUMHMM fails to build on tokay2 with the following error message: " there is no package called 'Biobase' ". http://bioconductor.org/checkResults/3.5/bioc-LATEST/ BUMHMM/tokay2-buildsrc.html There are no problems with other platforms. It seems that many packages are encountering

Re: [Bioc-devel] Build error: Dependency 'Biobase' is not available

Hi Shraddha, On 10/26/2016 11:12 AM, Shraddha Pai wrote: Hello BioC developers, I'm not sure why the nightly build of my package IdeoViz is reporting this error on tokay (see message below). It seems to me that not having Biobase installed is such a fundamental problem that the package should

Re: [Bioc-devel] Build error: Dependency 'Biobase' is not available

Hi Hervé, Thank you for the feedback, that makes sense. Thanks also to all the BioC system admins for maintaining such a large system of interdependent packages. BioC makes complex genomics data analysis so easily accessible to community researchers. Regards, Shraddha On Wed, Oct 26, 2016 at

[Bioc-devel] Build error: Dependency 'Biobase' is not available

Hello BioC developers, I'm not sure why the nightly build of my package IdeoViz is reporting this error on tokay (see message below). It seems to me that not having Biobase installed is such a fundamental problem that the package should have been flagged when it first got submitted (sometime in

Re: [Bioc-devel] build error only occurs in window system

du<mailto:jianhong...@umassmed.edu>>, Lihua Julie Zhu <julie@umassmed.edu<mailto:julie@umassmed.edu>>, "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel

Re: [Bioc-devel] build error only occurs in window system

dhutch.org>> >> Date: Thursday, July 7, 2016 3:15 PM >> To: Jianhong Ou >><jianhong...@umassmed.edu<mailto:jianhong...@umassmed.edu>>, Lihua Julie >>Zhu <julie@umassmed.edu<mailto:julie@umassmed.edu>>, >>"bioc-devel@r-project.org<

Re: [Bioc-devel] build error only occurs in window system

Don't bother. The issue is a long-standing one and very difficult to reproduce which is why it has not been fixed. It happens sporadically so the solution is to wait for the next day's build and it will clear itself up. Dan On July 7, 2016 11:05:22 AM PDT, "Ou, Jianhong"

Re: [Bioc-devel] build error only occurs in window system

Hi Julie, You could try to install windows 10 in a virtualBox for debugging. virtualBox: https://www.virtualbox.org/wiki/Downloads Windows 10: https://www.microsoft.com/en-us/software-download/windows10/ Yours Sincerely, Jianhong Ou TEL: 508-856-5379 LRB 608 Bioinformatician of

[Bioc-devel] build error only occurs in window system

Dan, I recently noticed that GUIDEseq page has a error build status at http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html. Oddly, the error only occurs in the window server. Is this something related to the window server solvable by the core team, or should I change something to

Re: [Bioc-devel] Build error in released version

This is my opinion. I think the class should have a very general structure. Depending on the assay, users may be particularly interested in the original case described by Herve (alignments on opposite strands, same chromosome), but I dont think it should be enforced. We have first(), last(),

Re: [Bioc-devel] Build error in released version

Thanks for the clarification , Hervé! That makes sense to me! I prefer option b and c. Best, Julie > On Jul 5, 2016, at 6:05 PM, Hervé Pagès wrote: > > Hi Julie, > >> On 07/05/2016 01:03 PM, Zhu, Lihua (Julie) wrote: >> Dear Herve, >> >> Thank you so much for the

Re: [Bioc-devel] Build error in released version

Hi Julie, On 07/05/2016 01:03 PM, Zhu, Lihua (Julie) wrote: Dear Herve, Thank you so much for the detailed explanation and quick fix! When fusion occurs, the 2 alignments in a pair could be on different chromosomes. Not sure what is the best way to handle this situation. If set seqnames to *,

Re: [Bioc-devel] Build error in released version

Dear Herve, Thank you so much for the detailed explanation and quick fix! When fusion occurs, the 2 alignments in a pair could be on different chromosomes. Not sure what is the best way to handle this situation. If set seqnames to *, then the mapping location is lost. Maybe set seqnames to one

Re: [Bioc-devel] Build error in released version

Hi Julie, The GAlignmentPairs container didn't support discordant strand until BioC 3.4 (current devel). In the current release (and in previous versions of BioC) strand discordance was not supported. I recently fixed a bug in the released version of GenomicAlignments where the strand() getter

[Bioc-devel] Build error in released version

Hi, I just noticed that the released version of GUIDEseq failed at build stage, which did not occur previously and I did not make any change to the release version. The error points to the GAlignmentPairs container. Is this an intended change and should I modify my code to accommodate the

Re: [Bioc-devel] Build error on Moscato2 for mzR

:bioc-devel-boun...@r-project.org] On Behalf Of > Steffen Neumann > > Sent: Thursday, April 07, 2016 11:03 AM > > To: Samuel Wieczorek; mailman, bioc-devel > > Subject: Re: [Bioc-devel] Build error on Moscato2 for mzR > > > > Hi Samuel, > > > > On Do, 2016-

Re: [Bioc-devel] Build error on Moscato2 for mzR

Thursday, April 07, 2016 11:03 AM > To: Samuel Wieczorek; mailman, bioc-devel > Subject: Re: [Bioc-devel] Build error on Moscato2 for mzR > > Hi Samuel, > > On Do, 2016-04-07 at 10:28 +0200, Samuel Wieczorek wrote: > [...] >> >> which needs the mzR package. >>

Re: [Bioc-devel] Build error on Moscato2 for mzR

; mailman, bioc-devel Subject: Re: [Bioc-devel] Build error on Moscato2 for mzR Hi Samuel,  On Do, 2016-04-07 at 10:28 +0200, Samuel Wieczorek wrote: [...] > > which needs the mzR package. > The latter package has build error since a few days and this > propagates errors on the other pac

Re: [Bioc-devel] Build error on Moscato2

Sent: Thursday, April 7, 2016 1:28:00 AM > Subject: [Bioc-devel] Build error on Moscato2 > Hi > my packages (DAPAR and Prostar) are dependant of the package MSnbase > which needs the mzR package. > The latter package has build error since a few days and this propagates > errors o

Re: [Bioc-devel] Build error on Moscato2 for mzR

Hi Samuel,  On Do, 2016-04-07 at 10:28 +0200, Samuel Wieczorek wrote: [...] > > which needs the mzR package. > The latter package has build error since a few days and this > propagates  > errors on the other packages. We're painfully aware of the build failure of mzR. I opened an issue  for it

[Bioc-devel] Build error on Moscato2

Hi my packages (DAPAR and Prostar) are dependant of the package MSnbase which needs the mzR package. The latter package has build error since a few days and this propagates errors on the other packages. What will happen for these other packages in the next release if mzR is not correctly

Re: [Bioc-devel] BUILD error on moscato2: package not installed for 'arch=x64'

- Original Message - > From: "THEVENOT Etienne 207099" <etienne.theve...@cea.fr> > To: "bioc-devel" <bioc-devel@r-project.org> > Sent: Thursday, March 10, 2016 10:57:05 PM > Subject: [Bioc-devel] BUILD error on moscato2: package not installed

[Bioc-devel] BUILD error on moscato2: package not installed for 'arch=x64'

Dear Bioconductor Team, I got the following BUILD error on moscato2 (demo example in my vignette suggesting the 'xcms' package): Error: processing vignette 'ropls.Rnw' failed with diagnostics: chunk 27 Error : package 'xcms' is not installed for 'arch = x64' Execution halted How shall I

Re: [Bioc-devel] build error, piano package

- Original Message - From: Leif Väremo var...@chalmers.se To: bioc-devel@r-project.org Sent: Tuesday, April 21, 2015 11:38:31 PM Subject: [Bioc-devel] build error, piano package Dear developers, I am hoping someone can help me with this issue: The piano package in the devel

[Bioc-devel] build error, piano package

Dear developers, I am hoping someone can help me with this issue: The piano package in the devel branch runs into an error while building on Bioconductor Linux (zin1), however everything is fine in the release branch (zin2). Since the release and devel versions are identical at the moment I

[Bioc-devel] Build error for DESeq2 dev causing error in other package builds

Hello, I am the maintainer of a Bioconductor package called 'HTSFilter' that imports DESeq2. On today's build report, I see that my package (as well as DESeq2 and all of the other packages that import it) is showing an error message which seems to arise from a recent change in the DESeq2 code

Re: [Bioc-devel] Build error for DESeq2 dev causing error in other package builds

hi Andrea, I sent out an email to bioc-devel at the same time as you :) https://stat.ethz.ch/pipermail/bioc-devel/2015-April/007269.html I think this might be fixed already, but I didn't have time to try out GenomicRanges 1.19.51 yet. I will try soon, and if this doesn't fix it, I have a hack

Re: [Bioc-devel] Build error for DESeq2 dev causing error in other package builds

On 04/03/2015 04:37 AM, Andrea Rau wrote: Hello, I am the maintainer of a Bioconductor package called 'HTSFilter' that imports DESeq2. On today's build report, I see that my package (as well as DESeq2 and all of the other packages that import it) is showing an error message which seems to arise

[Bioc-devel] build error on RIPSeeker

Dear developer community, There seems to be an error in the nightly build of my package `RIPSeeker' (0.99.8) on the Mac OS X Leopard (10.5.8) / i386 (petty) (message pasted below). The error occurs in the Vignette demo. However, I have not updated my package and cannot figure out why that