Re: [Bioc-devel] Can we still patch a broken package in 3_11

hanges will be included > in the upcoming release. > > thank you. > > Lori Shepherd > Bioconductor Core Team > Roswell Park Comprehensive Cancer Center > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bioc

[Bioc-devel] Can we still patch a broken package in 3_11

-LATEST/OUTRIDER/ Would it be still possible to patch it to make it work again? I can understand if the branch 3_11 is fixed and you do not want to touch it again. I attached the patch if you decide to change it. Best, Christian -- Christian Mertes | PhD Student / Lab Administrator Gagneur Lab

Re: [Bioc-devel] git push permission denied

nd you should have access to it now. > > Best, > > Nitesh > > > > > On Jun 2, 2020, at 12:34 AM, Christian Mertes > > wrote: > > > > Dear Bioc team, > > > > I tried to push an update to my FRASER package, but was not > > s

[Bioc-devel] git push permission denied

on this. Best, Christian -- Christian Mertes | PhD Student / Lab Administrator Gagneur Lab - Computational Genomics I12 - Department of Informatics Technical University of Munich Boltzmannstr. 3, 85748 Garching, Germany mer...@in.tum.de | https://in.tum.de/gagneurlab

Re: [Bioc-devel] 'OUTRIDER' Bioconductor package

report. > > Martin > > On 10/11/19, 7:33 PM, "Bioc-devel on behalf of Christian Mertes" > wrote: > > Dear Bioc Team, > > I noticed already the error and I'm not completely sure why this is > happening. On appveyor it is going through with

Re: [Bioc-devel] 'OUTRIDER' Bioconductor package

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

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

educedDims" for this object of class "daFrame" >> >>    CTDquerier: >>      bfcadd() failed; see warnings() >> >>    specL: >>      pandoc.exe: Out of memory >> >>    These errors don't seem related to the conv

[Bioc-devel] read.table fails with https protocol

;, nrows=10)[,1:10], row.names=1) data.frame(fread(paste0("http://;, URL),  sep="\t", nrows=10)[,1:10], row.names=1) I guess my solution is to use http or move to use fread or curl. But I think the clean way is to use read.table or? Best, Christian -- Christian Mertes PhD Stud

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

ou should be able to > achieve the same effect when using the png device(s) in R, and that > will make everything more portable anyway. > > On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes <mailto:mer...@in.tum.de>> wrote: > > Dear BioC team, > > I jus

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

.Rnw' failed with diagnostics: no lines available in input --- failed re-building 'OUTRIDER.Rnw' SUMMARY: processing the following file failed: 'OUTRIDER.Rnw' Error: Vignette re-building failed. Execution halted -- Christian Mertes PhD Student / Lab Administrator Gagneur lab Computational

Re: [Bioc-devel] Fwd: failing package OUTRIDER

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 no

Re: [Bioc-devel] Cairo Error on MacOS on Bioc 3.9

> the binary from CRAN. Once CRAN makes the binary available your package > will build. > > Valerie > > > > > > On 12/14/18 4:37 AM, Christian Mertes wrote: >> Dear Bioconductor team, >> >> I noticed that my package OUTRIDER and also some oth

[Bioc-devel] Cairo Error on MacOS on Bioc 3.9

Also the same error came up in earlier versions already and was then solved. https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007643.html I guess this is rather an issue of the test server. But if you need more information on this, please let me know. Best regards, Christian Mertes

Re: [Bioc-devel] Roxygen documentation under windows

]{BiocParallelParam}} It >> should remedy the issue. >> >> >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> El

[Bioc-devel] Roxygen documentation under windows

Hey all, I have a question. My package builds perfectly on Linux and MacOS, but fails to link my documentation correctly on Windows, which results in a warning. The exact error which I get is: Rd warning:

Re: [Bioc-devel] Dependency to PEER

Hi Martin Morgen, Thanks for the suggestion with the vignette. This will do it. Best, Christian > On 26. Sep 2018, at 04:07, Martin Morgan wrote: > > > > On 09/25/2018 07:07 PM, Christian Mertes wrote: >> Hi, >> thanks for the answers. >> Since we only

Re: [Bioc-devel] Dependency to PEER

>> It is a major weakness of PEER that it has not been submitted to a standard >> repository. Of course, that is up to the PEER developers, but the community >> should put pressure on them. >> >> On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes wrote: >> >>>

[Bioc-devel] Dependency to PEER

Hi all, Im the developer of OUTRIDER. Our package normalises RNA-seq count data and finds expression outliers within the population. During the development we compared our approach against PCA and PEER. The later one is a well established method to normalise RNA-seq data.