date:20190418

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

2019-04-18 Thread Pages, Herve

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 message in the new miRspongeR package is not needed and might 
only confuse your users.

Also the miRSM package now should import miRspongeR instead of miRsponge.

Thanks,

H.


On 3/6/19 16:06, Junpeng Zhang via Bioc-devel wrote:
> Thanks, Nitesh.
> Regards,
> Junpeng ZhangSchool of Engineering, Dali UniversityWebsite: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Junpeng-5FZhang3=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=raF3P8uAjLTGnVSrMUOXE0XtnN5LLclAD-PrragYPbI=
>
>  On Wednesday, March 6, 2019, 11:30:23 PM GMT+8, Turaga, Nitesh 
>  wrote:
>   
>   Hi Juanpeng,
> You should now have access to miRspongeR on git.bioconductor.org. Before 
> making any changes, please make sure to “sync” the GitHub 
> andgit.bioconductor.org repositories for miRspongeR.
> Link to instructions: 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=n4sbuqwWP6Osif_UEZSHjwpzATAjhuMO7-_a7tIV3dE=
> Best,
> Nitesh
>
>
> On Mar 5, 2019, at 8:19 PM, Junpeng Zhang  wrote:
> Hi Nitesh,
> Sorry for this thing.
> I have added the .onLoad function in the zzz.R file. Please check the commits 
> both today and yesterday.
> If you have further issues, please let me know. Thanks.
> Regards,
> Junpeng ZhangSchool of Engineering, Dali UniversityWebsite: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Junpeng-5FZhang3=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=raF3P8uAjLTGnVSrMUOXE0XtnN5LLclAD-PrragYPbI=
>
> On Wednesday, March 6, 2019, 4:11:52 AM GMT+8, Turaga, Nitesh 
>  wrote:
>
> Hi Junpeng,
> Yes it is possible to do this.
> 1. We will first deprecate your package miRsponge in the devel version of 
> Bioconductor.
> a) You will need to add .onLoad function, which points users to the new 
> package ‘miRspongeR’.
> The .onLoad function goes in the zzz.R file, and it will throw a package 
> deprecation message point users to the new package.
> b) Push these changes to the package ongit.bioconductor.org
>
> 2. Once these changes are pushed, please reply to this email, and we’ll give 
> you access to the new package miRspongeR.
> NOTE: Make sure you make only deprecation commits to miRsponge from this 
> point forth. All package development you want to actually take forward will 
> go in the new package (which you will get access to)
> Best,
> Nitesh
>
>
> On Mar 5, 2019, at 9:33 AM, Junpeng Zhang via Bioc-devel 
>  wrote:
> Dear Bioconductor developers,
>
> I am maintaining an R/Bioconductor package called miRsponge.  However, the 
> name miRsponge is very similar with an existing database (miRSponge, 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bio-2Dbigdata.net_miRSponge_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=lTEZY9DTTECbF_gakiLXba-WAOWPyrGKtseOi_mSDek=).
>  To make the package more distinct, I want to change the the name of package 
> into miRspongeR. The name miRspongeR will be more distinct.
> Is it possible to change the the name of R package that is already published 
> on Bioconductor?
> Sorry for this thing. Thanks in advance!
> Regards,
> Junpeng ZhangSchool of Engineering, Dali UniversityWebsite: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Junpeng-5FZhang3=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=raF3P8uAjLTGnVSrMUOXE0XtnN5LLclAD-PrragYPbI=
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cbx6n5EQdF8XyDXsfl8jAn23rMl0Wr_KlygZJlotE68=DW9KkZM7tNY7yAATsKGTsSSzlRovLut31Jv3vFK7dOY=
>
>
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer.

[Bioc-devel] Community generated annotation deadline is April 24th

2019-04-18 Thread Van Twisk, Daniel

Hello Bioconductor Community,


Just a reminder that the community generated annotation package deadline is 
April 24th. Please submit these packages to me by then.


Thank you!


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.9 Orgdbs and TxDbs available

2019-04-18 Thread Van Twisk, Daniel

Hello Bioconductor Community!


The new OrgDb and TxDbs for the Bioconductor 3.9 release are now available.



The new Orgdbs are:


GO.db_3.8.0.tar.gz
org.Ag.eg.db_3.8.0.tar.gz
org.At.tair.db_3.8.0.tar.gz
org.Bt.eg.db_3.8.0.tar.gz
org.Ce.eg.db_3.8.0.tar.gz
org.Cf.eg.db_3.8.0.tar.gz
org.Dm.eg.db_3.8.0.tar.gz
org.Dr.eg.db_3.8.0.tar.gz
org.EcK12.eg.db_3.8.0.tar.gz
org.EcSakai.eg.db_3.8.0.tar.gz
org.Gg.eg.db_3.8.0.tar.gz
org.Hs.eg.db_3.8.0.tar.gz
org.Mm.eg.db_3.8.0.tar.gz
org.Mmu.eg.db_3.8.0.tar.gz
org.Pf.plasmo.db_3.8.0.tar.gz
org.Pt.eg.db_3.8.0.tar.gz
org.Rn.eg.db_3.8.0.tar.gz
org.Sc.sgd.db_3.8.0.tar.gz
org.Ss.eg.db_3.8.0.tar.gz
org.Xl.eg.db_3.8.0.tar.gz
PFAM.db_3.8.0.tar.gz




The new TxDbs are:


TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.5.tar.gz
TxDb.Celegans.UCSC.ce11.ensGene_3.4.5.tar.gz
TxDb.Celegans.UCSC.ce11.refGene_3.4.5.tar.gz
TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.5.tar.gz
TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.5.tar.gz
TxDb.Drerio.UCSC.danRer10.refGene_3.4.5.tar.gz
TxDb.Drerio.UCSC.danRer11.refGene_3.4.5.tar.gz
TxDb.Ggallus.UCSC.galGal4.refGene_3.4.5.tar.gz
TxDb.Ggallus.UCSC.galGal5.refGene_3.4.5.tar.gz
TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.5.tar.gz
TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.5.tar.gz
TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.5.tar.gz
TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.5.tar.gz
TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.5.tar.gz
TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.5.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.5.tar.gz
TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.5.tar.gz
TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.5.tar.gz
TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.5.tar.gz



Lastly, a reminder that all community generated annotation packages are to be 
submitted by April 24th for the upcoming release.


Thank you!


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

2019-04-18 Thread Neumann, Steffen

Hi, 

thanks everyone for the input, I now have a few more leads to follow. 
It would be great to have a general single package builder 
even for existing packages to check if one has no direct access 
to the failing architecture.

https://win-builder.r-project.org/ is discouraging BioC package upload,
and might have a different build environment. 

Let's see if we get a working Rdisop for easter. 
A nice weekend everyone, 
yours,
Steffen

On Thu, 2019-04-18 at 13:25 +, Martin Morgan wrote:
> I second the idea of reproducing with the Windows build commands,
> which have to do more than 'just' build for a particular
> architecture. One might test the hypothesis that it is staged install
> that is causing the problem with 
> 
>   StagedInstalll: no
> 
> in the DESCRIPTION file.
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2019-04-18 Thread Pages, Herve

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:

https://bioconductor.org/checkResults/3.9/bioc-LATEST/universalmotif/tokay2-checksrc.html

The universalmotif.Rcheck/tests_i386/testthat.Rout.fail file is:

R version 3.6.0 beta (2019-04-12 r76385) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(universalmotif)
>
> test_check("universalmotif")
-- 1. Error: viewing motif stacks works (@test_view_motifs.R#39)  --
could not find function "merge_motifs_get_offset"
1: view_motifs(c(m1, m2)) at testthat/test_view_motifs.R:39
2: lapply(seq_along(mot.mats)[-1], function(x) {
   y <- merge_motifs_get_offset(mot.mats[[1]], mot.mats[[x]], method, 
min.overlap,
   mot.ics[[1]], mot.ics[[x]], min.mean.ic, normalise.scores)
   merge_add_cols(y)
   y
   })
3: FUN(X[[i]], ...)

== testthat results  ===
OK: 193 SKIPPED: 2 FAILED: 1
1. Error: viewing motif stacks works (@test_view_motifs.R#39)

Error: testthat unit tests failed
Execution halted

I'm not sure why the merge_motifs_get_offset() function cannot be found when R 
is running in i386 mode. I see that merge_motifs_get_offset() is implemented in 
C++ and integrated to the universalmotif package using the Rcpp machinery (with 
RcppExports.cpp and RcppExports.R files). The package also uses a top-level 
Makefile and a src/Makevars file. Overall this looks like a relatively 
complicated setup. Could it be that the issue with the unit test is somehow 
related to some subtle issue with this setup? Unfortunately I'm not familiar 
with the Rcpp/RcppExports.cpp/RcppExports.R machinery so I'm not able be 
provide more help, sorry. Hopefully someone on the list with more experience 
will be able to help.

Unlikely to be related but FWIW I noted that "[[: not found" is displayed 
during installation:

https://bioconductor.org/checkResults/3.9/bioc-LATEST/universalmotif/tokay2-install.html

(once during the "install for i386" step and once during the "install for x64" 
step). Don't know if that's something that you should worry about or not 
though...

Best,
H.

On 4/9/19 12:31, Benjamin Tremblay wrote:

Hi,

R CMD check on the tokay2 machine fails due to an error in running tests from 
testthat in the devel branch of my package universalmotif with no indication as 
to why. Here is the output from R CMD check:

* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(universalmotif)
  >
  > test_check("universalmotif")
  == testthat results  
===
  OK: 211 SKIPPED: 1 FAILED: 0
** running tests for arch 'x64' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
And here is the testthat.Rout.fail file:

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(testthat)
library(universalmotif)

test_check("universalmotif")

== testthat results  ===
OK: 211 SKIPPED: 1 FAILED: 0
Is there any way for me to know what is going on?

Thanks,

Benjamin Tremblay
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4TnLfmbrqNHzJ9eUGNM_B-Uv8yp47su45HLGzZmQFaw=VvVcCPb17b20Lj8eW6qyU5UCMsjZ__ABfaWESPWEhuM=

--
Hervé Pagès

Re: [Bioc-devel] Dashes in GFF attributes

2019-04-18 Thread Marcel Ramos

Hi Valentino,

You will have to provide more details concerning the issue.
It may be as simple as removing the dashes with `gsub` before using 
`featureCount`.

Please review the posting guidelines for a better idea on how to get help:

https://bioconductor.org/help/support/posting-guide/

And consider using `support.bioconductor.org` to post.

Best regards,

Marcel


On 4/17/19 10:51 AM, Valentino Giudice wrote:

Hi, I hope this is the right place to write.

The featureCount function of Rsubread doesn't work if the GFF file contains
dashes in the 9th column.
https://github.com/Bioconductor/BiocManager/issues/45

I was told to write in bioc-devel.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Dashes in GFF attributes

2019-04-18 Thread Valentino Giudice

Hi, I hope this is the right place to write.

The featureCount function of Rsubread doesn't work if the GFF file contains
dashes in the 9th column.
https://github.com/Bioconductor/BiocManager/issues/45

I was told to write in bioc-devel.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

2019-04-18 Thread Martin Morgan

I second the idea of reproducing with the Windows build commands, which have to 
do more than 'just' build for a particular architecture. One might test the 
hypothesis that it is staged install that is causing the problem with 

  StagedInstalll: no

in the DESCRIPTION file.

Makevars is evaluated on Windows, unless there's a Makevars.win. cleanup is 
not, but cleanup.win is.

Martin

On 4/18/19, 8:38 AM, "Bioc-devel on behalf of Mike Smith" 
 wrote:

I can reproduce the error using R-3.6.0beta and running the following two
steps to replicate the Bioc builder commands:

R CMD build --keep-empty-dirs --no-resave-data Rdisop
rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir &&
C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch
--build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz

Bit of a guess, and I don't know why this would have changed, but
the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files
referenced in the error.  If these were produced for 64-bit architecture
then they'll fail when the build process tries to use them for the 32-bit
binary.  Perhaps your Rcpp edits removed some cleanup code that was there
before?  I note there's no Makevars.win or cleanup.win but my memory is a
bit fuzzy on whether only versions with *.win will be run on Windows or if
that's just a way to provide alternative code if needed.

On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen 
wrote:

> Hi,
>
> with the next release coming up, I am out of wits regarding the failure at
>
> 
http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
> which exists since before April this year, when we committed
> some changes to get rid of the RcppClassic dependency.
>
> Max Helf succeeded to build locally on windows without problem.
>
> So it seems that Rdisop has issues with the BioC windows build
> environment, but I totally fail to see the reason.
>
> Could it be the new staged installation ?
> But I wouldn't know why that'd affect the compile/linking.
>
> The issue is tracked at
> https://github.com/sneumann/Rdisop/issues/13
>
> Any help/pointers appreciated.
>
> Yours,
> Steffen
>
> --
>
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

2019-04-18 Thread Mike Smith

I can reproduce the error using R-3.6.0beta and running the following two
steps to replicate the Bioc builder commands:

R CMD build --keep-empty-dirs --no-resave-data Rdisop
rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir &&
C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch
--build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz

Bit of a guess, and I don't know why this would have changed, but
the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files
referenced in the error.  If these were produced for 64-bit architecture
then they'll fail when the build process tries to use them for the 32-bit
binary.  Perhaps your Rcpp edits removed some cleanup code that was there
before?  I note there's no Makevars.win or cleanup.win but my memory is a
bit fuzzy on whether only versions with *.win will be run on Windows or if
that's just a way to provide alternative code if needed.

On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen 
wrote:

> Hi,
>
> with the next release coming up, I am out of wits regarding the failure at
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
> which exists since before April this year, when we committed
> some changes to get rid of the RcppClassic dependency.
>
> Max Helf succeeded to build locally on windows without problem.
>
> So it seems that Rdisop has issues with the BioC windows build
> environment, but I totally fail to see the reason.
>
> Could it be the new staged installation ?
> But I wouldn't know why that'd affect the compile/linking.
>
> The issue is tracked at
> https://github.com/sneumann/Rdisop/issues/13
>
> Any help/pointers appreciated.
>
> Yours,
> Steffen
>
> --
>
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

2019-04-18 Thread Neumann, Steffen

Hi,

with the next release coming up, I am out of wits regarding the failure at 
http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
which exists since before April this year, when we committed 
some changes to get rid of the RcppClassic dependency.

Max Helf succeeded to build locally on windows without problem. 

So it seems that Rdisop has issues with the BioC windows build
environment, but I totally fail to see the reason. 

Could it be the new staged installation ? 
But I wouldn't know why that'd affect the compile/linking. 

The issue is tracked at 
https://github.com/sneumann/Rdisop/issues/13

Any help/pointers appreciated. 

Yours,
Steffen

-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

[Bioc-devel] Community generated annotation deadline is April 24th

[Bioc-devel] Bioconductor 3.9 Orgdbs and TxDbs available

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

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

Re: [Bioc-devel] Dashes in GFF attributes

[Bioc-devel] Dashes in GFF attributes

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

10 matches

Site Navigation

Mail list logo

Footer information