[Bioc-devel] Have trouble in push to master branch

Hi, I am trying to fix bug in my package. However, I got declined message: git push upstream master Counting objects: 38, done. Delta compression using up to 8 threads. Compressing objects: 100% (26/26), done. Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done. Total 38 (delta 30),

Re: [Bioc-devel] Have trouble in push to master branch

; Best regards, > > Julie > > On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" wrote: > >Hi Jianhong, > > > >I’m looking into it now. > > &

[Bioc-devel] Ask help to install gs tokay2 build/check

Hi, Is it possible to install ghostscript in tokay2 for development package build? Yours Sincerely, Jianhong Ou Email: jianhong...@duke.edu Bioinformatician II Department of Cell Biology Duke University School of Medicine Durham, NC, 27710 Confidentiality Notice: T

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

My package motifStack import grImport which is depend on ghostscript. Jianhong. From: Kasper Daniel Hansen Date: Friday, November 2, 2018 at 8:55 AM To: "Jianhong Ou, Ph.D." Cc: bioc-devel Subject: Re: [Bioc-devel] Ask help to install gs tokay2 build/check Perhaps explain why On

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

ifStack is clean so I'm not sure what happened in the previous day's builds. The build report for today, Nov 2, should post within the next hour and motifStack should be green. Valerie On 11/2/18 6:05 AM, Jianhong Ou, Ph.D. wro

Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

Hi Sunyong, plotMotifLogo does not compatible with par now. Please use grid to plot the multiple panels in one canvas. I am working on this but it takes time. Jianhong. On 4/23/19, 12:47 AM, "Bioc-devel on behalf of Shin, Sunyoung" wrote: Dear all, I got an error message: inva

Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

, valueOnly = TRUE)), y=unit(1.5, "lines"), gp=gpar(col = "blue", lwd = 1.5, xpd=NA), arrow=arrow(length = unit(0.1, "inches"), angle = 15, ends = "last")) grid.text("3'", x=unit(1, "npc") - unit(1, "li

[Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi, The package trackViewer get check error in tokay1 (windows) say: Error in library(org.Hs.eg.db) : there is no package called 'org.Hs.eg.db' How could I debug this error? Thank you for your help. Yours Sincerely, Jianhong Ou [[alternative HTML version deleted]]

Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

It is for a long time. Since last development version (BioC 3.9). Jianhong. From: "Shepherd, Lori" Date: Friday, June 14, 2019 at 9:29 AM To: "Jianhong Ou, Ph.D." , Michael Lawrence via Bioc-devel Subject: Re: CHECK ERROR in tokay1 for BioC 3.10 How long as this ERROR oc

Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

e Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(org.Hs.eg.db) Error in library(org.Hs.eg.db) : there is no package called 'org.Hs.eg.db' Execution halted On 6/14/19, 9:31 AM, "Bioc-devel o

Re: [Bioc-devel] How to speed up GRange comparision

Try dist=distance(query, subject) dist==0 ? On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working" wrote: Hello, I have two big GRanges objects and want to search for an overlap of the first range of query with the first range of subject. Then take the second rang

Re: [Bioc-devel] How to speed up GRange comparision

Oh, I forget that. Thank you for reminder. Then how about: distance(query, narrow(subject, start=2, end=-2)) == 0 ? On 1/29/20, 12:40 PM, "Pages, Herve" wrote: On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote: > Try > dist=distance(query, subjec

[Bioc-devel] Got timeout for machv2 BUILD

Hi, Hope you are doing well. I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have limited information how to debug. Could you share your suggestion? Thank you. Yours Sincerely, Jianhong

Re: [Bioc-devel] Got timeout for machv2 BUILD

Hi, I got timeout for my package motifStack in machv2. But I don't know what cuased the issue. Any help would be greatly appreciated. Jianhong. From: Jianhong Ou, Ph.D. Sent: Wednesday, April 15, 2020 7:53 AM To: bioc-devel@r-project.org Subject: Got ti

Re: [Bioc-devel] Got timeout for machv2 BUILD

Hi Stefano, Thank you for your share. Jianhong. From: Stefano de Pretis Date: Friday, April 17, 2020 at 3:18 PM To: "Jianhong Ou, Ph.D." Cc: "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] Got timeout for machv2 BUILD HI, We solved a similar issue for the INSPEcT

Re: [Bioc-devel] Got timeout for machv2 BUILD

Best, H. On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote: > Hi, > > I got timeout for my package motifStack in machv2. But I don't know what cuased the issue. > > Any help would be greatly appreciated. > > Jianhong.

Re: [Bioc-devel] Got timeout for machv2 BUILD

rly Mac builds of R 4.0. > > Please keep an eye on tomorrow's report (Saturday) and let me know if the > TIMEOUT is still there. > > Thanks, > H. > > >> On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote: >> Hi Herve, >> Thank you for your help. >> Jianh

[Bioc-devel] How to handle Empty reply from server from httr package

Hi all, Sometime my package got "Empty reply from server" error when I using httr package. The pseudo-code I used to handle error is like this: library(httr) APIurl <- "https://www.ebi.ac.uk/proteins/api/features?offset=0&size=-1&reviewed=true&types=DNA_BIND%2CMOTIF%2CDOMAIN&taxid=9606&accessio

[Bioc-devel] Ask for help to debug the error on riesling1

Hi, The trackViewer package got error on Windows Server since version 1.27.4. I am totally lost to figure it out by myself. The current error message listed in building system is: * creating vignettes ... ERROR --- re-building 'changeTracksStyles.Rmd' using rmarkdown --- finished re-building '

Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi Alan, Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. Hope this help. You may want to add one more step after check and before pkgdown to push to your dockerhub by: - name: push to docker - uses: docker/build-push-action@v1 with: username: ${{

Re: [Bioc-devel] Ask for help to debug the error on riesling1

Hi Herv�, Thank you for the information. I will try to figure out. Jianhong. From: Herv� Pag�s Sent: Wednesday, April 7, 2021 1:54 AM To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1 Hi

Re: [Bioc-devel] Ask for help to debug the error on riesling1

nformation? Jianhong. From: Martin Morgan Sent: Wednesday, April 7, 2021 2:16 PM To: Jianhong Ou, Ph.D. ; Hervé Pagès ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1 I followed these steps, more or less, to configu

[Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

Hi All, I got warning message in windows building like: Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/help/$<-,track-method.html': Invalid argument I used RoxygenNote to create the Rd file and the note I wrote li

Re: [Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Jianhong Ou, Ph.D. Sent: Wednesday, April 14, 2021 3:11 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] How t

[Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

Hi all, In most recent build I got error message: shape of 'skeleton' is not compatible with 'NROW(flesh)' And I have trouble in repeating the error by Bioconductor/bioconductor_docker:devel. I am asking will the bioconductor_docker will update soon or I should install the newest development

Re: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

Hi Lori, Thank you so much for the message. Jianhong. From: Kern, Lori Sent: Thursday, May 6, 2021 8:09 AM To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org Subject: Re: How to repeat the error: shape of 'skeleton' is not compatible with 'NRO

[Bioc-devel] Question about IRanges for coordinates greater than 536870912

Hi All, Recently I encountered issues with IRanges that the coordinates greater than 536870912. Is there any easy solution to extract the information from bam file for the range greater than 2^29 via Rsamtools or GenomicAlignments? And does Rsamtools support CRAI or CSI index formats? Thank yo

[Bioc-devel] ENCODExplorer is not available in release and development version

Dear Charles and maintainers of ENCODEExplorer, The ENCODExplorer package is not available in release and development version. ENCODExplorer package is an important package for my current work. I hope it can be fixed as soon as possible. Thank you for your help. Yours Sincerely, Jianhong Ou

Re: [Bioc-devel] ENCODExplorer is not available in release and development version

Hi Lori, Thank you so much for letting me know that. I will have a try. Jianhong. From: Kern, Lori Sent: Wednesday, June 23, 2021 8:34 AM To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org Subject: Re: ENCODExplorer is not available in release and development

[Bioc-devel] Need help for debug on palomino3

Hi all, The package I maintained got error in Windows Server 2022 Datacenter / x64. However I don�t have any windows system to debug. What is the best way to repeat the errors in palomino3? Any suggestion is welcome. Thank you for your help. Jianhong. [[alternative HTML version deleted

Re: [Bioc-devel] Need help for debug on palomino3

Thank you Hervé. I will take a try. Looks like the first year is free. J. From: Hervé Pagès Date: Thursday, March 24, 2022 at 1:36 PM To: Jianhong Ou, Ph.D. , bioc-devel@r-project.org Subject: Re: [Bioc-devel] Need help for debug on palomino3 Hi Jianhong, Is there any possibility that you