Re: [Bioc-devel] Build error for cfTools

: Monday, March 31, 2025 2:50 PM To: Kern, Lori Cc: Martin Grigorov ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Build error for cfTools Hi Lori, Thanks for your quick response. The build error seems to stem from an environment issue with tensorflow=2.10.0. I was hoping the Bioconduc

Re: [Bioc-devel] Build error for cfTools

prehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of RAN HU > > *Sent:* Monday, March 31, 2025 2:14 PM > *To:* Martin Gr

Re: [Bioc-devel] Build error for cfTools

Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of RAN HU Sent: Monday, March 31, 2025 2:14 PM To: Martin Grigorov Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Build error for

Re: [Bioc-devel] Build error for cfTools

Hi, I noticed that there is still a build error on Windows Server for cfTools: https://bioconductor.org/checkResults/devel/bioc-LATEST/cfTools/palomino7-buildsrc.html. Does this prevent Windows users from installing or using the R package? If so, I’d really appreciate the opportunity to work toge

Re: [Bioc-devel] Build error: missing downloadthis dependency

: Sunday, November 24, 2024 7:48 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error: missing downloadthis dependency Hello all, I am reaching out regarding an issue with two of the packages I maintain, EpiCompare and the recently accepted MotifPeeker, which fail on Iconway due to a

[Bioc-devel] Build error: missing downloadthis dependency

Hello all, I am reaching out regarding an issue with two of the packages I maintain, EpiCompare and the recently accepted MotifPeeker, which fail on Iconway due to a missing dependency. The missing package in question is *downloadthis*, which is available on CRAN. I would like to note that both p

Re: [Bioc-devel] Build error: missing perl xml module

progress at https://github.com/Bioconductor/BBS/issues/421. > > > Jennifer Wokaty (they/them) > > Waldron Lab at CUNY SPH > Bioconductor Core Team > -- > *From:* Bioc-devel on behalf of > Spencer Nystrom > *Sent:* Tuesday, September 24, 2024 1

Re: [Bioc-devel] Build error: missing perl xml module

From: Bioc-devel on behalf of Spencer Nystrom Sent: Tuesday, September 24, 2024 10:16 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error: missing perl xml module * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and a

[Bioc-devel] Build error: missing perl xml module

Hi all, I maintain the `{memes}` package that interfaces with the MEME Suite toolkit. I just noticed a failing build in devel because the meme suite was installed on the builders (thank you!!), and it is missing a perl module. ``` Can't locate XML/Parser/Expat.pm in @INC (you may need to install

Re: [Bioc-devel] Build error for cfTools

Hi Martin, Thank you very much for your efforts in solving the problem! I believe kunpeng2 is a relatively new platform, so we did not previously notice the build error. The problem is understandable, and I appreciate that we’ve worked to address it to make most platforms working. Best, Ran On

Re: [Bioc-devel] Build error for cfTools

Hi Ran, Do you remember how it was solved before (for kunpeng2) ? https://anaconda.org/conda-forge/tensorflow does not provide linux-aarch64 build even for 2.17.0 in the conda-forge channel. Your package uses 2.10.0. The anaconda channel does provide it - https://anaconda.org/anaconda/tensorflow,

[Bioc-devel] Build error for cfTools

Hi, I am the maintainer of the cfTools package. I found cfTools have build errors on palomino7/8 and kunpeng2 for BioC 3.19 and 3.20, which appear to be caused by an environment issue related to a Python dependency. This has happened before and was solved. Could you help me solve this again? And i

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

swell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets 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 Subj

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

hepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Julien Wollbrett Sent: Monday, August 5, 2024 7:45 AM To:

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

M 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. 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

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. Th

[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 libr

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 c

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 ob

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 also

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 > https://blog.bioconductor.org/posts/2023-06-09-deb

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 issue

[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 https://bioconductor.org/checkResults/devel/bioc-L

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

Team 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 un

[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 ‘musm

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 in

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(" https://g

[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 resolv

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, > > It

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. H

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 4.

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 B

[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 vignette

[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 report

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 > rmarkdow

[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

ehensive Cancer 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-de

[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: * chec

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 com

[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 ok.

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

on 3 (but will be in the near future)� The > >>> windows error can be ignored for now. > >>> > >>> > >>> > >>> Lori Shepherd > >>> > >>> Bioconductor Core Team > >>> > >>> Roswell Park Cancer

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

Bioinformatics >>> >>> Elm & Carlton Streets >>> >>> Buffalo, New York 14263 >>> >>> >>> *From:* Bioc-devel on behalf of >>> Simon Dirmeier &

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

on behalf of 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

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

t; Department of Biostatistics & 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@

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

m: Bioc-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 tok

[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 changes

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 believ

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 i

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 seria

[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, when

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 05

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 of

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 t

[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: si

Re: [Bioc-devel] Build Error processing vignette

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Kucukural, Alper 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 proces

[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 Univers

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 compati

[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? http://bioconductor.org/checkResults

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 file(con,

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 09:

[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. pandoc.ex

Re: [Bioc-devel] Build error on tokay2

Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Alina Selega 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

[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 t

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 h

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 3:3

[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 20

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

>to the header and > >Suggests: rmarkdown (...) > >to the DESCRIPTION for a BiocStyle'd vignette > >Martin > > >> >> Cheers, >> H. >> >>> >>> Best, >>> >>> Julie >>> >>> From: Dan Tenenbaum >>

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

med.edu>>, Lihua Julie Zhu mailto:julie@umassmed.edu>>, "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] build error only occurs in window system Don't bother. The issue is a long-standing one

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

3:15 PM >> To: Jianhong Ou >>mailto:jianhong...@umassmed.edu>>, Lihua Julie >>Zhu mailto:julie@umassmed.edu>>, >>"bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" >>mailto:bioc-devel@r-project.org>> >> Subject: Re: [B

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

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

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

>, Lihua Julie Zhu mailto:julie@umassmed.edu>>, "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] build error only occurs in window system Don't bother. The issue is a long-standing one and

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" wrote: >Hi Julie, >

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 Bioinformatics

[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 m

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(), sec

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 detailed explanation and qu

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 of

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 wa

[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 chan

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

mation on Bioc build servers on Sunday. > > Details here > > https://github.com/sneumann/mzR/issues/36 > > Best wishes, > > Laurent > > > Best > > > > Peter > > > > -Original Message- > > From: Bioc-devel [mailto:bioc-devel-boun

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

> 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, 2016-04-07 at 10:28 +0200, Samuel Wieczorek wrote: > [...] >> >> which needs the mzR package

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

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. > The latter package has build error since a few days and this > propagates errors on the

Re: [Bioc-devel] Build error on Moscato2

The mzR maintainers are aware of the issue, which has to do with the new windows toolchain. They are working on it. Dan - Original Message - > From: "Samuel Wieczorek" > To: "bioc-devel" > Sent: Thursday, April 7, 2016 1:28:00 AM > Subject: [Bioc-deve

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