[Bioc-devel] DMRcate: TIMEOUT

2017-05-30 Thread Tim Peters
ached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.0 Best, Tim -- Tim Peters, PhD Bioinformatics Research Officer | Epigenetics Research Laboratory | Genomics and Epigenetics Division Garvan Instit

Re: [Bioc-devel] DMRcate: TIMEOUT

2017-05-31 Thread Tim Peters
ackage build process? Doing so might give you some hints about which >> code >> blocks are the culprits. > > Also > > > Stangle("DMRcate.Rnw") > Writing to file DMRcate.R > > source("DMRcate.R", echo=TRUE, max=Inf) > > to generate the

[Bioc-devel] Access permissions for DMRcate

2018-09-11 Thread Tim Peters
e "consensus", but not "DMRcate". Can I add DMRcate myself through some process, or alternatively can I get an admin to do so please? Best, Tim -- === Tim Peters, PhD Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology Division Garvan In

Re: [Bioc-devel] Access permissions for DMRcate

2018-09-13 Thread Tim Peters
unt and your information (i.e., package permissions) should by synced up. Valerie On 09/11/2018 08:14 PM, Tim Peters wrote: Hi BioC, I'm attempting to sync the my repo https://github.com/timpeters82/DMRcate-devel with Bioconductor using the process here: http://bioconductor.org/developer

Re: [Bioc-devel] Access permissions for DMRcate

2018-09-14 Thread Tim Peters
t.pet...@garvan.org.au<mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au>. I've removed the @csiro.au account and your information (i.e., package permissions) should by synced up. Valerie On 09/11/2018 08:14 PM, Tim Peters wrote: Hi

[Bioc-devel] minfi::makeGenomicRatioSetFromMatrix() Windows mem alloc error

2019-04-29 Thread Tim Peters
opers investigate this please? The purpose of calling makeGenomicRatioSetFromMatrix() is to access the chromosome position and ID from a methylation matrix with probe IDs as rownames. DMR.plot() also needs the beta values so I am killing 2 birds with 1 stone with this call. Best, Tim -- ===

[Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

2019-08-21 Thread Tim Peters
to download and update Bioconductor, and then I can sync the new version of DMRcate please? Best, Tim -- === Tim Peters, PhD Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology Division Garvan Institute of Medical Research 384 Victoria St

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

2019-09-12 Thread Tim Peters
2/9/19 11:51 pm, Turaga, Nitesh wrote: Thanks Tim. The assigned reviewer will review your package and provide suggestions as needed. Best, Nitesh On Sep 12, 2019, at 3:15 AM, Tim Peters <mailto:t.pet...@garvan.org.au> wrote: Hi Nitesh, Thanks, I have transformed DMRcatedata into an E

Re: [Bioc-devel] check fails on arch 'i386'

2019-10-17 Thread Tim Peters
packages. Best, Kasper On Thu, Oct 17, 2019 at 4:08 AM Tim Peters mailto:t.pet...@garvan.org.au>> wrote: Hi Hervé (and Reka), I am having much the same problem on tokay1 with DMRcate (https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html). I've gone through a

Re: [Bioc-devel] check fails on arch 'i386'

2019-10-17 Thread Tim Peters
__ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=2BO1kFpXuH1gpxwLxHae_ELnR7g