Re: [Bioc-devel] credential not recognized when git clone my packages

treets Buffalo, New York 14263 From: Bioc-devel on behalf of Zhu, Lihua (Julie) Sent: Saturday, January 9, 2021 11:16 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] credential not recognized when git clone

[Bioc-devel] credential not recognized when git clone my packages

Hi all, I encountered the following error when trying to use git clone or git push for g...@git.bioconductor.org:packages/CRISPRseek # git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into

Re: [Bioc-devel] help with accessing CRISPRseek

Never mind, I recovered my key and that fixed it. Thanks! Best regards, Julie On 6/18/19, 5:39 PM, "Bioc-devel on behalf of Zhu, Lihua (Julie)" wrote: Hi, I am trying to use git to access CRISPRseek. However, it asks for passphrase. I was able to do this withou

[Bioc-devel] help with accessing CRISPRseek

Hi, I am trying to use git to access CRISPRseek. However, it asks for passphrase. I was able to do this without entering the passphrase a couple of months ago. Could you please help? Thanks! git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into 'CRISPRseek'... Enter

Re: [Bioc-devel] Cannot reset credentials password

Lori, I checked and confirmed that the email did not get sent to the spam folder. FYI, I can receive others' posts without any problem. Thank you very much for your help! Best regards, Julie On 3/6/19, 9:53 AM, "Bioc-devel on behalf of Shepherd, Lori" wrote: Have you checked that the

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

;Turaga, Nitesh" wrote: Please try now. > On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie) wrote: > > Nitesh, > > I encountered the same issue with CRISPRseek pack

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

Nitesh, I encountered the same issue with CRISPRseek package. Could you please help? Thanks! To git.bioconductor.org:packages/CRISPRseek.git ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/CRISPRseek.git'

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

thub RELEASE_3_6 to Bioconductor’s RELEASE_3_6. Best, Nitesh > On Mar 29, 2018, at 2:10 PM, Zhu, Lihua (Julie) <julie@umassmed.edu> wrote: > > Nitesh, > > I will try it. Since it is a released version, I thought I will first

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

conductor. > > Let me know if this works. > > Best, > > Nitesh > > >> On Mar 28, 2018, at 4:23 PM, Zhu, Lihua (Julie) <julie@umassmed.edu> >> wrote: >> >> Nitesh, >> >> I am trying to fix the following erro

[Bioc-devel] FW: GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Nitesh, I am trying to fix the following error in the released version by adding the correct encoding in the DESCRIPTION file. However, I encountered the following message. Could you please help? Thanks! Best regards, Julie git push upstream RELEASE_3_6 Counting objects: 401, done. Delta

Re: [Bioc-devel] git push complains non-existing files being too big

ry of any traces of them. These files were in your older RELEASE versions. You should be able to work on them now. You need to get a fresh clone of the repo. Best, Nitesh > On Mar 26, 2018, at 4:03 PM, Zhu, Lihua (Julie) <julie@umassmed.edu> wrot

[Bioc-devel] Help: git push complains non-existing files being too big

/LihuaJulieZhu/GUIDEseq.git ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to 'https://github.com/LihuaJulieZhu/GUIDEseq.git' From: "Zhu, Lihua (Julie)" <julie@umassmed.edu> Date: Monday, October 19, 2015 at 1:32 PM T

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Dear Bioc Core members, I received the following error report, although I have not updated GUIDEseq for a while. Error in iconv(x[ind], "latin1", "ASCII", sub = "byte") : object 'ind' not found Is this a problem from a dependent package that parses ASCII

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

Thanks so much, Lori! Best, Julie From: "Shepherd, Lori" <lori.sheph...@roswellpark.org> Date: Friday, August 25, 2017 at 1:58 PM To: "Zhu, Lihua (Julie)" <julie@umassmed.edu>, "bioc-devel@r-project.org" <bioc-devel@r-project.org&g

[Bioc-devel] Question : GitHub-Commit changes to the released branch

Hi, I need to fix a bug in the development and released version of CRISPRseek. So far, I have successfully updated the dev version of CRISPRseek following the guides at https://www.bioconductor.org/developers/how-to/git/maintain-bioc-only/. I have a couple of question regarding commit changes

Re: [Bioc-devel] git / svn transition: ssh keys

d like read-only access you can use HTTPS. ``` git clone https://git.bioconductor.org/packages/CRISPRseek ``` Best, Nitesh > On Aug 21, 2017, at 11:25 AM, Zhu, Lihua (Julie) <julie@umassmed.edu> wrote: > > Dear Nitesh, &g

Re: [Bioc-devel] git / svn transition: ssh keys

Dear Nitesh, I submitted my ssh keys. However, I cannot download my packages from github. Could you please help? Thanks! # juliezhumac2017:Trunk ZHUJ$ git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into 'CRISPRseek'... Permission denied (publickey). fatal: Could not read

Re: [Bioc-devel] build error only occurs in window system

ch.org> wrote: >Hi Julie, > >On 07/07/2016 12:36 PM, Zhu, Lihua (Julie) wrote: >> Thanks Dan! I did came across a similar post a few years ago regarding >>its non-reproducibility >>http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-output-f &

[Bioc-devel] build error only occurs in window system

Dan, I recently noticed that GUIDEseq page has a error build status at http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html. Oddly, the error only occurs in the window server. Is this something related to the window server solvable by the core team, or should I change something to

Re: [Bioc-devel] Build error in released version

Thanks for the clarification , Hervé! That makes sense to me! I prefer option b and c. Best, Julie > On Jul 5, 2016, at 6:05 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > > Hi Julie, > >> On 07/05/2016 01:03 PM, Zhu, Lihua (Julie) wrote: >> Dear H

Re: [Bioc-devel] Build error in released version

ot clear what seqnames() or granges() should >do in that case. Maybe return/set the seqname to * but that means >introducing * as a special seqlevel. Still need to think about the >implications of this. > >Cheers, >H. > >On 07/01/2016 02:23 PM, Zhu, Lihua (Julie) wrote: >> Hi,

[Bioc-devel] Build error in released version

Hi, I just noticed that the released version of GUIDEseq failed at build stage, which did not occur previously and I did not make any change to the release version. The error points to the GAlignmentPairs container. Is this an intended change and should I modify my code to accommodate the

[Bioc-devel] inquiry about possibility of package name change

Martin, The lab, who developed the GUIDE-seq protocol, just published a python tool called guideseq in Nature Biotechnology, which is too similar to our Bioconductor package name GUIDEseq. I am wondering if there is an easy way to change the package name, or perhaps give it an alias to point

Re: [Bioc-devel] import except on Window Machine

exceptions more difficult to maintain. A better syntax for this >case might have been: > >import(cranPackage, override=values) > >But we have to live with except= for now. > >Michael > >On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie) ><julie@umassmed.edu&g

Re: [Bioc-devel] import except on Window Machine

ch.org>, "Michael Lawrence" >>>>< >>>> >> lawrence.mich...@gene.com>, "bioc-devel" >>>> >> > <bioc-devel@r-project.org> >>>> >> > Sent: Monday, April 11, 2016 10:03:52 AM >>>>

Re: [Bioc-devel] import except on Window Machine

.3/Resources/library/bioCancer� * restoring previous �/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer� Exited with status 1 When I used R 3.4, I get : unfortunately, Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help Bioconductor does not yet support R version

Re: [Bioc-devel] import except on Window Machine

Thanks, Dan! Best, Julie On 4/11/16 12:22 PM, "Dan Tenenbaum" wrote: >The windows machine is still running an older version of R that does not >support this NAMESPACE syntax. I will update it this week. >Dan > > >- Original Message - >> From: "Lihua Zhu"

[Bioc-devel] import except on Window Machine

Michael, For some reason, adding except clause in import in the NAMESPACE file gives error on window server, although it runs fine on Linux and Mac OS X. http://bioconductor.org/checkResults/devel/bioc-LATEST/CRISPRseek/moscato2-buildsrc.html Here is the line that gives error.

Re: [Bioc-devel] namespace question

;>> >>>>>> >>>>>> On Thu, Mar 31, 2016 at 4:00 PM, <luke-tier...@uiowa.edu> wrote: >>>>>>> >>>>>>> >>>>>>> I don't think you want to separate it from the import. Better to >>>>&g

Re: [Bioc-devel] namespace question

of having conflicting names, is it not appropriate then >>>to use >>> the "package::function" form for calling a particular function? >>> >>> On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence >>><lawrence.mich...@gene.com> >>>

Re: [Bioc-devel] namespace question

em pragmatic to importFrom(hash, ...) since it has so few functions. On Thu, Mar 31, 2016 at 6:54 AM, Zhu, Lihua (Julie) <julie@umassmed.edu<mailto:julie@umassmed.edu>> wrote: > Sorry. I meant values. > > replacing previous import ŒIRanges::values¹ by Œhash::val

Re: [Bioc-devel] namespace question

>On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Julie) ><julie@umassmed.edu> wrote: >> Michael, >> >> I have the same user case as Kasper. Another example is that both >>IRanges >> and hash packages have hash. I need to use the hash from the hash >&

Re: [Bioc-devel] namespace question

l] namespace question No, as far as I know. I asked about this on R-devel a long time ago; would be nice to have importFromExcept() Best, Kasper On Wed, Mar 30, 2016 at 3:19 PM, Zhu, Lihua (Julie) <julie@umassmed.edu<mailto:julie@umassmed.edu>> wrote: Hi, Is there a function

[Bioc-devel] namespace question

Hi, Is there a function to import all the exported objects from a package except a few named ones in NAMESPACE file? For example, I would like to import all the functions in S4Vectors except fold. Is there a way to specify this without listing all other functions using importFrom? Many

[Bioc-devel] FW: [bioc] A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for

Valerie, Could you please help answer the multicore problem the user experienced with? FYI, I used parLapply to replace lapply when multicore = TRUE. Thanks! Best regards, Julie From: "alexgraehl [bioc]" > Reply-To:

Re: [Bioc-devel] new Bioconductor team members

Jim and Brian, welcome to the Bioconductor community! Marc, Sonail and Paul, many thanks for all your help! You will be missed! Best regards, Julie > On Sep 8, 2015, at 6:24 PM, Obenchain, Valerie > wrote: > > In September the Bioconductor project