Re: [Bioc-devel] Windows build error

elps. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of RAN HU Sent: Thursday, April 20, 2023 2:58 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Windows build error ***ATTENTION: This email came f

Re: [Bioc-devel] Windows build error

Dear BioC team, I wonder if this error is caused by your Windows environment. Or is there anything I can do to fix it? If this Windows build error is not solved, will cfTools still be included in the 3.17 release version? Thanks in advance! Best, Ran On Tue, Apr 18, 2023 at 4:46 PM RAN HU wro

[Bioc-devel] Windows build error

Hi all, My package cfTools has recently been accepted. I just found that there is a build error on Windows: Multiple platform build/check report for BioC 3.17 - BUILD results for cfTools on palomino3 (bioconductor.org)

Re: [Bioc-devel] Windows specific error during CHECK

! -Ursprüngliche Nachricht- Von: Hervé Pagès Gesendet: Dienstag, 26. Oktober 2021 21:53 An: Felix Ernst ; bioc-devel@r-project.org Betreff: Re: [Bioc-devel] Windows specific error during CHECK Hi Felix, On 26/10/2021 12:10, Felix Ernst wrote: Hi Bioc-Team, I have got a problem with an error on Windows

Re: [Bioc-devel] Windows specific error during CHECK

Thanks Herve! -Ursprüngliche Nachricht- Von: Hervé Pagès Gesendet: Dienstag, 26. Oktober 2021 21:53 An: Felix Ernst ; bioc-devel@r-project.org Betreff: Re: [Bioc-devel] Windows specific error during CHECK Hi Felix, On 26/10/2021 12:10, Felix Ernst wrote: > Hi Bioc-Team, > &g

Re: [Bioc-devel] Windows specific error during CHECK

Hi Felix, On 26/10/2021 12:10, Felix Ernst wrote: Hi Bioc-Team, I have got a problem with an error on Windows, which I am not able to debug. http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-checksrc.html The testthat.out.fail output doesn't indicate any problems and the te

[Bioc-devel] Windows specific error during CHECK

Hi Bioc-Team, I have got a problem with an error on Windows, which I am not able to debug. http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-checksrc.html The testthat.out.fail output doesn't indicate any problems and the testthat.out on other systems looks the same. Can som

Re: [Bioc-devel] Windows-specific Function Not Found Error

Hello, Ah, I had a few different uses of MultiAssayExperiment::colData in a particular function of the package, but one line had only colData without the scoping in front. I wish that R error messages displayed R file names and line numbers more often. -- Da

Re: [Bioc-devel] Windows-specific Function Not Found Error

Remember that Windows doesn�t have �forked� parallelism; all processes are running in separate processes where the functions in use need to be made explicitly available. Likely you can emulate this error on non-windows by using �SnowParam()� instead of MulticoreParam(), e.g., > library(Summari

[Bioc-devel] Windows-specific Function Not Found Error

Good day, I see a checking failure for ClassifyR for Windows Server 2019 only. The error is Error: BiocParallel errors 4 remote errors, element index: 1, 4, 6, 8 6 unevaluated and other errors first remote error: could not find function "colData" Is there anything I can change in my code

[Bioc-devel] Windows Not Connected to Internet?

Hi - I recently updated the PoTRA release 3_13, but see that the same error is showing up. ## ## ### ### Running command: ### ### chmod a+r Po

Re: [Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of stefano Sent: Wednesday, May 5, 2021 8:55 PM To: bioc-devel Subject: [Bioc-devel] Windows build. err

[Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

Hello, the package ppcseq fails on windows build (Multiple platform build/check report for BioC 3.13 - INSTALL report for ppcseq on riesling1 (bioconductor.org) ) because of the lack of RcppParallel in the wi

[Bioc-devel] Windows build warnings from basilisk configure file

Hi, I have submitted the package dasper as an additional package to megadepth to Bioconductor 3.12: https://github.com/Bioconductor/Contributions/issues/1696 dasper interfaces into python using the Bioconductor package basilisk. I’ve included a configure file in the root of the dasper package f

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

rk 14263 From: Charles Warden Sent: Monday, May 4, 2020 12:04 PM To: Herv�� Pag��s ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi Everybody, It looks like the error is now fi

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

ge. > > Thank You, > Charles > > -Original Message- > From: Hervé Pagès > Sent: Tuesday, April 28, 2020 10:32 AM > To: Charles Warden ; Shepherd, Lori > ; 'bioc-devel@r-project.org' > > Subject: Re: [Bioc-devel] Windows Development Build Error Messa

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

harles Warden ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi Charles, The error you get on Windows is because your Perl script integrate_island.pl fails on this platform. It contains the following code: if (($os

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Tuesday, April 28, 2020 10:32 AM To: Charles Warden ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi Charles, The error you get on Windows is because your Perl script integrate_island.pl fails on this

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Y&s=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEGgHdGQ&e=> So, if I understand everything, I think this is OK. Thanks Again, Charles *From:*Shepherd, Lori *Sent:* Tuesday, April 28, 2020 5:29 AM *To:* Charles Warden ; Hervé Pagès ; 'bioc-devel@r-project.org' *Subject:* Re:

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Warden ; Hervé Pagès ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP I can investigate more on the windows machine after we are done with the release (later this week -- possibly early next) I would highly recommend not rev

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

nt of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Charles Warden Sent: Monday, April 27, 2020 12:27 PM To: Herv�� Pag��s ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: RE: [Bioc-devel] Windows

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

ONE (COHCAP) The downloaded source packages are in ‘C:\Users\Charles\AppData\Local\Temp\Rtmp88lsk0\downloaded_packages’ Installation path not writeable, unable to update packages: boot, class, foreign, KernSmooth, MASS, nnet, spatial I

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

12:23 PM To: Charles Warden ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpec

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Charles, On 4/23/20 10:19, Charles Warden wrote: My guess was that creating the temporary file in the working directory instead of another folder might help. FWIW here are 2 important reasons for writing temporary stuff to tempdir() instead of the current working directory: 1. tempdir(

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

20 12:00 PM To: 'bioc-devel@r-project.org' mailto:bioc-devel@r-project.org>> Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi, I noticed that I received a few error messages in the Windows

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, April 23, 2020 8:00 AM To: Charles Warden ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP Thank you f

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Warden Sent: Wednesday, April 22, 2020 12:00 PM To: 'bioc-devel@r-project.org' Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi, I noticed that I received a few error messages in the Windows build for COHCAP: http://secure-

[Bioc-devel] Windows Development Build Error Message for COHCAP

Hi, I noticed that I received a few error messages in the Windows build for COHCAP: http://bioconductor.org/checkResults/devel/bioc-LATEST/COHCAP/tokay2-buildsrc.html I changed the default settings to avoid an earlier error message (again, just on Windows), but I am currently getting an error m

Re: [Bioc-devel] Windows only vignette error - any ideas?

matics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of > Christopher John > Sent: Wednesday, December 4, 2019 2:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Windows o

Re: [Bioc-devel] Windows only vignette error - any ideas?

Buffalo, New York 14263 From: Bioc-devel on behalf of Christopher John Sent: Wednesday, December 4, 2019 2:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Windows only vignette error - any ideas? Hi Since this morning I am getting an error for the

[Bioc-devel] Windows only vignette error - any ideas?

Hi Since this morning I am getting an error for the Windows build only of my M3C package, shown below. Could anyone help please? Thanks, Chris * checking for file 'M3C/DESCRIPTION' ... OK * preparing 'M3C': * checking DESCRIPTION meta-information ... OK * installing the package to build vignet

[Bioc-devel] Windows vignette build error "execution failed with error code 4"

Dear all, My package is almost ready to be accepted but now i am getting weird building error on Windows. It works without error on Linux and OS X. I have tried many many things. But I could not figured out. The error is: Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), c

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 > mail

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

Hi, Valerie! Thanks for looking into the problem! I hope it’ll work out. Erik On 16 Mar 2019, at 22:51, Valerie Obenchain mailto:obenchain.vale...@gene.com>> wrote: It doesn't look like it was the patch - the error is still there. I'll look in to this some more. Valerie On Fri, Mar 15, 2019

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

It doesn't look like it was the patch - the error is still there. I'll look in to this some more. Valerie On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain wrote: > Hi Erik, > I think the problem was introduced in a contributed patch applied to > VariantAnnotation in devel. I've reverted the pa

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

Hi Erik, I think the problem was introduced in a contributed patch applied to VariantAnnotation in devel. I've reverted the patch and expect VariantAnnotation (and downstream packages) to clear up on Windows with tomorrow's builds. Valerie On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius wrote: > H

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

Hi, My seqCAT package recently broke building on the Windows platform, which I assume has to do with changes to the VariantAnnotation package (upon which seqCAT depends). The error (which comes during the creation of the vignette) looks like this: Quitting from lines 102-112 (seqCAT.Rmd) Error

Re: [Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

Ops, ok, thanks. Should have reread the documentation. Thanks Bernat El 01/10/2018 a las 2:00, Dario Strbenac escribió: > Good day, > > The import of BigWig files does not work on Windows and is documented. > Execute ?BigWigFile-class and notice in the Description section: "These > functions

Re: [Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

Good day, The import of BigWig files does not work on Windows and is documented. Execute ?BigWigFile-class and notice in the Description section: "These functions do not work on Windows.". -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia __

[Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

Hi all, I've got a windows only error in one example of one of my packages (karyoploteR). The erroring function uses rtracklayer::import to load some data from a BigWig file with wig.data <- rtracklayer::import(data, format = "bigWig", selection=plot.region[i]) where plot.region[i] is

Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

Hi Val, I think I achieved some resolution, if not total clarity. It's to do with the encoding of the of the two path variables: > Encoding(path1) [1] "unknown" > Encoding(path2) [1] "UTF-8" I don't understand why recursive calls to normalizePath() changes the encoding, but the combination of H

Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

Hi Mike, Is this still an issue or has it been resolved? Val On 05/22/2018 02:19 PM, Mike Smith wrote: In trying to diagnose this issue at https://support.bioconductor.org/p/108548/ I've found some weird behaviour with Windows, normalizePath(), and non-ASCII characters. Essentially, if I run no

[Bioc-devel] Windows, normalizePath(), and non-ASCII characters

In trying to diagnose this issue at https://support.bioconductor.org/p/108548/ I've found some weird behaviour with Windows, normalizePath(), and non-ASCII characters. Essentially, if I run normalizePath() recursively on a path that contains 'é' (I haven't tried other characters) something 'chang

Re: [Bioc-devel] Windows

conductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> ________ >> From: Bioc-de

Re: [Bioc-devel] Windows

-devel on behalf of Mike Smith > > Sent: Monday, April 16, 2018 6:13:38 AM > To: Rainer Johannes; bioc-devel > Subject: Re: [Bioc-devel] Windows on Tokay2> > > Martin mentioned that he changed the wording in > https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e

Re: [Bioc-devel] Windows

rk 14263 From: Bioc-devel on behalf of Mike Smith Sent: Monday, April 16, 2018 6:13:38 AM To: Rainer Johannes; bioc-devel Subject: Re: [Bioc-devel] Windows Martin mentioned that he changed the wording in https://github.com/wch/r-sourc

Re: [Bioc-devel] Windows

Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes wrote: > Thanks Mike, > > I somehow missed the discussion you mentione

Re: [Bioc-devel] Windows

Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that works on Linux and macOS should also work on Windows - otherwise what's the matter of the alias? Interestingly, on my Windows test mac

Re: [Bioc-devel] Windows

Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html I think you should be able to get round it by including the name of Rd file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}

[Bioc-devel] Windows

Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages. Example: we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and mac

[Bioc-devel] Windows devel builds: NAs in BUILD BIN

Hi, You may have noticed occasional 'NA' values in the 'BUILD BIN' column on the the Windows (tokay2) build report. These NAs appear when the build products from the nodes (Windows and Mac) are not available to the postrun script on master (Linux). This 'unavailability' can be due to network co

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 11:23 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan >> mailto:martin.mor...@roswellpark.org>> >> wrote: >> >> On 04/26/2017 10:34 AM, James W. MacD

Re: [Bioc-devel] Windows binaries for the new release?

On 04/26/2017 11:23 AM, James W. MacDonald wrote: On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan mailto:martin.mor...@roswellpark.org>> wrote: On 04/26/2017 10:34 AM, James W. MacDonald wrote: On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan mailto:martin.mor...@roswellp

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 10:34 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan >> mailto:martin.mor...@roswellpark.org>> >> >> wrote: >> >> On 04/26/2017 10:00 AM, James W. M

Re: [Bioc-devel] Windows binaries for the new release?

On 04/26/2017 10:34 AM, James W. MacDonald wrote: On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan mailto:martin.mor...@roswellpark.org>> wrote: On 04/26/2017 10:00 AM, James W. MacDonald wrote: I see the binaries on the respective web pages, but biocLite seems not to:

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 10:00 AM, James W. MacDonald wrote: > >> I see the binaries on the respective web pages, but biocLite seems not to: >> > > I'm not 100% sure but can you try again in a new R session? I think you

Re: [Bioc-devel] Windows binaries for the new release?

On 04/26/2017 10:00 AM, James W. MacDonald wrote: I see the binaries on the respective web pages, but biocLite seems not to: I'm not 100% sure but can you try again in a new R session? I think you have a cached version of the repository index. Martin biocLite() BioC_mirror: https://bioc

[Bioc-devel] Windows binaries for the new release?

I see the binaries on the respective web pages, but biocLite seems not to: > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21). installation path not writeable, unable to update packages: foreign Old packages: 'AnnotationDbi', 'Bio

Re: [Bioc-devel] Windows build error for outdated Shiny package

Dear Martin, Thanks very much. Best Regards, Chen Hao > On 24 Sep 2016, at 5:44 PM, Martin Morgan > wrote: > > On 09/24/2016 05:43 AM, Nuno Agostinho wrote: >> Good evening, >> >> I recently submitted a package to Bioconductor. Unfortunately, the Windows >> machine (moscato1) returned the f

Re: [Bioc-devel] Windows build error for outdated Shiny package

On 09/24/2016 05:43 AM, Nuno Agostinho wrote: Good evening, I recently submitted a package to Bioconductor. Unfortunately, the Windows machine (moscato1) returned the following error while building the package: Error : package 'shiny' 0.13.2 was found, but >= 0.14 is required by 'psichomics'

[Bioc-devel] Windows build error for outdated Shiny package

Good evening, I recently submitted a package to Bioconductor. Unfortunately, the Windows machine (moscato1) returned the following error while building the package: Error : package 'shiny' 0.13.2 was found, but >= 0.14 is required by 'psichomics' The issue related to the package in question is

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

Thanks Martin! Using mode='wb' solved the issue. On Sat, Jun 18, 2016 at 10:41 AM, Martin Morgan wrote: > On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I get the same error while hosting the data somewhere else or when using >> RawGit's url. That is: >> >>> library('downl

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote: Hi, I get the same error while hosting the data somewhere else or when using RawGit's url. That is: library('downloader') download(' http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata', destfile = 'test2.Rdata') load

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

Hi, I get the same error while hosting the data somewhere else or when using RawGit's url. That is: > library('downloader') > download(' http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata', destfile = 'test2.Rdata') > load('tes2t.Rdata') Error: ReadItem: unknown type 50, perh

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

I wonder if raw only means "raw after line return munging"? can you attach the file that gets downloaded via email? (off list is fine) On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres wrote: > Hi, > > I'm trying to figure out what is going wrong with an error that pops > up on Windows o

[Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

Hi, I'm trying to figure out what is going wrong with an error that pops up on Windows only. It's currently the only error for a package that I recently submitted to Bioc. The function is fairly simple: it downloads a Rdata file from the web and loads it. If I try to download and load the file wi

Re: [Bioc-devel] Windows build error: cannot open file 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpaEUpE0\xshell23645160444e': Permission denied

Dan - Original Message - > From: "Simon G Coetzee" > To: bioc-devel@r-project.org > Sent: Friday, August 21, 2015 11:10:37 AM > Subject: [Bioc-devel] Windows build error: cannot open file > 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpaEUpE0\xshell2364516044

[Bioc-devel] Windows build error: cannot open file 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpaEUpE0\xshell23645160444e': Permission denied

I am working on getting a package ready for Bioconductor called motifbreakR. http://bioconductor.org/spb_reports/motifbreakR_0.99.7_buildreport_20150818123558.html#moscato1_buildsrc_anchor This is the build report. My package has as part of it’s plotting function, the necessity of producing a te