Re: [Bioc-devel] Omada package failing due to removed dependency

devel to RELEASE_3_18 correct? Cheers, Sokratis On Tue, Apr 2, 2024 at 11:06 AM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Dear all, > > I am getting some warnings that the Omada package is failing. If I am > correct I need to make some changes to both the deve

Re: [Bioc-devel] Omada package failing due to removed dependency

and upload my new code)? Thanks in advance! Regards, Dr. Sokratis Kariotis On Fri, Feb 9, 2024 at 10:27 AM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Hey, > > Hope I find you well! I have pushed some changes in devel and (I believe) > in branch RELEASE_3_1

Re: [Bioc-devel] Omada package failing due to removed dependency

er Center > > > On Mon, Sep 11, 2023 at 10:05 PM Sokratis Kariotis < > sokratiskario...@gmail.com> wrote: > >> Hey, >> >> Will the package be ok for the new release even though I still get the >> same >> error? >> >> Cheers, >>

Re: [Bioc-devel] Omada package failing due to removed dependency

gt; > Best, > Mike > > On Thu, 17 Aug 2023 at 03:47, Sokratis Kariotis < > sokratiskario...@gmail.com> wrote: > >> Hey all, >> >> I can see all is green but I still get messages about failing builds and >> on >> the website shows build error. Do I s

Re: [Bioc-devel] Omada package failing due to removed dependency

onductor.org/checkResults/3.18/bioc-LATEST/omada/ > > Regards, > Martin > > On Thu, Aug 10, 2023 at 9:44 AM Sokratis Kariotis < > sokratiskario...@gmail.com> wrote: > >> Hey all, >> >> Is this fixed now? I think I can see all pass, but on the a

Re: [Bioc-devel] Omada package failing due to removed dependency

Hey all, Is this fixed now? I think I can see all pass, but on the actual website its still on error. Thanks! Cheers, Sokratis On Tue, Aug 1, 2023 at 4:25 PM Sokratis Kariotis wrote: > Hey, > > I believe I have resolved the conflicts and now can run: *git push > upstrea

Re: [Bioc-devel] Omada package failing due to removed dependency

prehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------ > *From:* Bioc-devel on behalf of > Sokratis Kariotis > *Sent:* Monday, July 31, 2023 7:27 AM > *To:* M

Re: [Bioc-devel] Omada package failing due to removed dependency

Tried but its Already up to date. On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, wrote: > Hi Sokratis, > > You need to do "git pull --rebase" before trying to push. > Most probably the version has been bumped upstream. > > Regards, > Martin > > On Mon, Jul

Re: [Bioc-devel] Omada package failing due to removed dependency

y of the exact error you're receiving. That might help > the team suggest a solution. > > Best regards, > Mike > > On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis < > sokratiskario...@gmail.com> wrote: > >> Hey both, >> >> I have edited the package code but

Re: [Bioc-devel] Omada package failing due to removed dependency

& Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Sokratis Kariotis > *Sent:* Monday, July 10, 2023 10:27 AM > *To:* Kern, Lori > *Cc:* Oleksii Nikolaienko ; > bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Omada

Re: [Bioc-devel] Omada package failing due to removed dependency

WjNwbJAPSnWq9G5setIw9CNP8avnjON5nhm_cjNhhn6s6kY07wwiSQ4sSQqsekskzOjhbm1/https%3A%2F%2Fmodalx.parisnanterre.fr%2Fmembres> > could take over maintenance, if you still bother to ask... > > Best, > Oleksii > > On Thu, 6 Jul 2023 at 06:23, Sokratis Kariotis > wrote: > > Hey, >

Re: [Bioc-devel] Omada package failing due to removed dependency

ffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of > Oleksii Nikolaienko > *Sent:* Thursday, June 29, 2023 5:36 AM > *To:* Sokratis Kariotis > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Omada package faili

[Bioc-devel] Omada package failing due to removed dependency

a archived version of it (or something similar) so I don't have to rewrite code based on new packages to avoid potentially inconsistencies? Please advise, thank you! Cheers, Dr. Sokratis Kariotis (PhD) Agency for Science, Technology and Research (A*STAR) Singapore Immunology Network (SIgN) Twitter: @

Re: [Bioc-devel] Update existing packages and change name

Hi all, After lots of tries we decided to follow your second suggestion. How can we stop the support for 32-bit windows? Cheers, Sokratis On 22 March 2018 at 15:14, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Sokratis, > > On 03/22/2018 06:13 AM, Sokratis Kariotis wrote:

Re: [Bioc-devel] Update data in data package, pcxnData

; Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk> >

Re: [Bioc-devel] Update data in data package, pcxnData

an eye on this to make sure its the case and please let us > know if you still are seeing issues next week. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlt

Re: [Bioc-devel] Update data in data package, pcxnData

can we bypass this? Thanks. Cheers, Sokratis On 27 March 2018 at 14:02, Sokratis Kariotis <s.kario...@sheffield.ac.uk> wrote: > Hey all, > > Thanks for the advice. I managed to fix the problem of no permissions! My > windows machine, after an update, changed the paths to my git

Re: [Bioc-devel] Update data in data package, pcxnData

0M1pZSEvB5qLCMKyD4Y > mTJ5aZkeCHh6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ== > > Are you sure you are using a private key which corresponds to any of these > public keys? I’d start with that. > > Best > > Nitesh > > > > On Mar 23, 2018, at 8:20 AM, Sokr

Re: [Bioc-devel] Update data in data package, pcxnData

ll Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > -- > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Shepherd, Lor

Re: [Bioc-devel] Update existing packages and change name

yee 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 b

[Bioc-devel] Update existing packages and change name

ance. Cheers -- Sokratis Kariotis Scientific Programmer Hidelab Sheffield Institute for Translational Neuroscience 385a Glossop Rd, Sheffield, S10 2HQ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.eth

Re: [Bioc-devel] Accepted packages can't find each other and fail build

s > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk> > *Sent:* Tuesday, October 31, 2017 11:20:39 AM > *To:* Shepherd, Lori > *Cc:* Hervé Pagès; Obenchain, Valerie; bioc-devel > > *Sub

Re: [Bioc-devel] Accepted packages can't find each other and fail build

both the release and devel versions of packages > for the release. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14

[Bioc-devel] Accepted packages can't find each other and fail build

find each other. In a previous pair of packages I am maintaining (pathprint and pathprintGEOData) I could use the first library in the data package vignette and building was fine. Is it necessary to remove library(pcxn) from pcxnData to get them build? Thanks in advance! Cheers -- Sokratis Kariotis

[Bioc-devel] new package submission (pcxn) Abnormal build result

a while it seems that whenever this problem arises its because of the igraph package installation. How can I deal with this? Thanks in advance. With Regards, Sokratis -- Sokratis Kariotis Scientific Programmer Hidelab Sheffield Institute for Translational Neuroscience 385a Glossop Rd, Sheffield, S10 2

[Bioc-devel] invalid PDF version and NULL vector errors in unchanged package

Hey all, I maintain 'pathprint', a package added to bioconductor in the last release. Now the BioC 3.6 BUILD ( http://bioconductor.org/checkResults/3.6/bioc-LATEST/pathprint/) is producing an error in all 3 platforms (despite it

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

, Sokratis On 30 March 2017 at 12:05, Martin Morgan <martin.mor...@roswellpark.org> wrote: > On 03/30/2017 05:21 AM, Sokratis Kariotis wrote: > >> Hey all, >> >> Thanks for the input! I followed Marcel's advice and included the library >> in my vignette. Also,

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

ou can resolve this issue by moving `SummarizedExperiment` to the > > Suggests field and > > > > including a `library(SummarizedExperiment)` call in your vignette. > > > > Best regards, > > > > Marcel > > > > > > On Mon, Mar 27, 2017 at 11:09 AM So

[Bioc-devel] Cannot find SummarizedExperiment's function assays()

Hey, I have submitted the package pathprintGEOData, which got accepted, but the build/check report is now producing the following error: *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics: chunk 1 Error in assays(result) : could not find function "assays"*