from:"Vladimir Kiselev"

Re: [Bioc-devel] there is no package called ‘BiocStyle’

2023-05-25 Thread Vladimir Kiselev

Great, many thanks for your help!

Cheers,
Vlad

On Thu, 25 May 2023 at 12:27, Kern, Lori 
wrote:

> Just to second Vince,  also in scmap you have two Suggests fields.  Please
> condense to one and it will likely resolve the issue.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Vincent Carey 
> *Sent:* Thursday, May 25, 2023 7:12 AM
> *To:* Vladimir Kiselev 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] there is no package called ‘BiocStyle’
>
> In SC3 you have Suggests: on two different lines in DESCRIPTION.  The
> second one supersedes the first, I suppose.
>
> On Thu, May 25, 2023 at 6:06 AM Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
> > Hello,
> >
> > Recently two of my packages (SC3 and scmap) started failing checks due
> to:
> > "there is no package called ‘BiocStyle'' error. I've added "Suggests:
> > BiocStyle" into my DESCRIPTION file both on the devel and RELEASE_3_17 as
> > was advised in the corresponding email and bumped the versions. However,
> my
> > packaging is still failing the Linux check:
> >
> >
> http://secure-web.cisco.com/1VwXooLQG-J8-lOVppcvzBb-IwxBCySNjqr-M5EJv38VPaKPb1GsShyAx2Yau4nNc0vmeH89e3ZCG3bVKdEqBNZ4kVVGPklC0cJKQA9QmNWhcg5epv6JCCRZq797CdcgFJG66ZAYnw8qArImZomyXn7hlmtRl1paBPpLxd5YzYM5txcx7X87MO1C6d-M-zWcA0mexA4yNvOKjs7O-5nVrNeTIlOaG0qr4tpyH7IaVSV8wsb9vli7JBdhgHYJdupx8WIUeT82EsduYgWoZLt4k_2piy_f1p1iBkps_YgykAovZH1ZNzTBVz4xKDaSgnJYA/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FSC3%2Fnebbiolo1-checksrc.html
> >
> >
> > Here is how the version and suggests fields look like in the DESCRIPTION
> > file of the RELEASE_3_17 branch:
> >
> > Version: 1.28.2
> > Suggests: BiocStyle
> >
> > Any suggestions/help would be really appreciated.
> >
> > Kind regards,
> > Vlad
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1wcuMaAtI6OlRaRNPYgn-w2VT6V-Ab1SgOjVboUnA12xBYFABlzv7A9c_NSEOH-3_0NVaQ6rHi8Ki2wZZ3sODJTs6k1GXThxbEDDyJuFwOrwtMYNh2qrKofLTyKoZYRLct4eqMyEXEvncY3VHE7CkvtbLYTVRBy5jSt5aLPJ4f5lsIJppDKrBoZKW_FLRSHvx1s6lESjYOVHI7jIa-NmoArnFrKy5-PrXHXT506CoUnkDVNJ4HHX-Hi-cCwaHfLT2mCLn1FqecAZGxu3VEc_UmXaG1PuAsQaHRVKk1UrDFRAQPDnvEEXtPwotQebGbcoa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:25}}

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[Bioc-devel] there is no package called ‘BiocStyle’

2023-05-25 Thread Vladimir Kiselev

Hello,

Recently two of my packages (SC3 and scmap) started failing checks due to:
"there is no package called ‘BiocStyle'' error. I've added "Suggests:
BiocStyle" into my DESCRIPTION file both on the devel and RELEASE_3_17 as
was advised in the corresponding email and bumped the versions. However, my
packaging is still failing the Linux check:
http://bioconductor.org/checkResults/release/bioc-LATEST/SC3/nebbiolo1-checksrc.html


Here is how the version and suggests fields look like in the DESCRIPTION
file of the RELEASE_3_17 branch:

Version: 1.28.2
Suggests: BiocStyle

Any suggestions/help would be really appreciated.

Kind regards,
Vlad

[[alternative HTML version deleted]]

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[Bioc-devel] Undefined slot classes warning

2018-12-17 Thread Vladimir Kiselev

Hello,

We have a warning related to defining an S4 object:
Warning: undefined slot classes in definition of "MyObject": index(class
"Rcpp_ModuleClass")

More details are here:
https://stackoverflow.com/questions/53814548/rcpp-class-wrapped-in-s4-object-warning

Could anyone please help?

Many thanks,
Vladimir

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Re: [Bioc-devel] Pandoc issues

2017-12-10 Thread Vladimir Kiselev

Thanks Herve!

Cheers,
Vlad

On Wed, Nov 29, 2017 at 6:38 PM Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi Vladimir,
>
> On 11/28/2017 01:25 PM, Vladimir Kiselev wrote:
> > Hi Herve,
> >
> > Thanks for your reply! scmap::getSankey() didn't really work in the
> > release, so I switched it off quite long ago by setting `eval = FALSE`.
> >
> > Regarding rmarkdown: I remember when I updated Pandoc I got a different
> > error from rmarkdown, then I googled it and found that it was related to
> > the changes in the new version of Pandoc (I can't find the link
> > now). The rmarkdown maintainer said he'd fixed it in the latest
> > version which is not the release version it. I have installed rmarkdown
> > from github (at the moment I have 1.8.3) and there was no error. They
> > probably forgot to update SystemRequirements.
>
> Wouldn't hurt to remind them about this.
>
> >
> > So, I suppose updating Pandoc on your side won't solve the problem
> > completely and we will need to wait until the new version of rmarkdown
> > is pushed to CRAN. At the moment I can probably switch Sankey diagrams
> > off in my vignette. The problem is I have just significantly updated it
> > and these diagrams are quite important now.
>
> Probably worth asking the rmarkdown folks whether they're planning
> to upload version 1.8.3 to CRAN soon, and to decide whether to switch
> off the diagrams or not based on what they say. Once rmarkdown 1.8.3
> (or higher) is on CRAN, I suggest that you update your Depends
> field to depend on rmarkdown >= 1.8.3. This will ensure that your
> users can also use scmap::getSankey(), not just our build machines.
>
> Note that if these diagrams are important, then you will probably need
> to consider porting your fixes to release. Your regular users use
> release, not devel.
>
> Best,
> H.
>
> >
> > Cheers,
> > Vlad
> >
> > On Tue, Nov 28, 2017 at 6:11 PM Hervé Pagès <hpa...@fredhutch.org
> > <mailto:hpa...@fredhutch.org>> wrote:
> >
> > Hi Vladimir,
> >
> > mmh... scmap::getSankey() used to work (and still works in the
> release
> > version of scmap) so I wonder what could have changed in the devel
> > version or in one of its dependencies to cause it to fail now...
> >
> > Anyway we'll look into updating pandoc to the latest version
> (currently
> > at version 1.19.1 on the Linux build machines).
> >
> > As for rmarkdown, it's a CRAN package and is currently at version 1.8
> > there:
> >
> > https://cran.r-project.org/web/packages/rmarkdown/index.html
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rmarkdown_index.html=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY=f7tzfxUzfieYY_eZcLQOwHRy2zo5gG7OykARY3AJ1uw=
> >
> >
> > That's the version installed on the build machines. Note that we only
> > install packages from CRAN or Bioconductor on these machines.
> >
> > If you think you found a bug in rmarkdown 1.8, or if you need a
> > feature that is only available in the devel version of rmarkdown,
> > I would suggest that you contact the rmarkdown developers by opening
> > an issue on GitHub:
> >
> > https://github.com/rstudio/rmarkdown/issues
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstudio_rmarkdown_issues=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY=m5Nj-tCYC2oES9jqql7akRGNlCzSBf8qtWU-TL5l0qA=
> >
> >
> > If the devel version of rmarkdown requires a higher version of pandoc
> > in order to work properly, then maybe you could suggest them to
> update
> > the SystemRequirements field, which is currently:
> >
> > SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pandoc.org=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY=0kGjllslkO0BS6iCNW4TIf2Qu4KjhpR2ZH939fc_o7Y=
> >
> >
> > (in both, rmarkdown 1.8 and 1.8.3)
> >
> > Best,
> > H.
> >
> >
> > On 11/28/2017 07:12 AM, Vladimir Kiselev wrote:
> >  > Hi,
> >  >
> >  > I am not able to plot Sankey diagrams using `googleVis` in the
> > vignette of
> >  > my package (scmap). Here is error message:
> >  >
>

[Bioc-devel] TLS error in vignette on all devel builds

2017-09-15 Thread Vladimir Kiselev

Hi,

In my package's (scmap) vignette I plot a Sankey digram using gvisSankey
function from googleVis package. It used to work and the digram was
plotted, but now there is this error (on devel branch -
http://bioconductor.org/checkResults/devel/bioc-LATEST/scmap/malbec1-buildsrc.html
):

pandoc: Could not fetch
https://www.google.com/jsapi?callback=displayChartSankeyID249e5aae1d64
TlsExceptionHostPort (HandshakeFailed Error_EOF) "www.google.com" 443
Error: processing vignette 'scmap.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67

I suppose it's some network issue, since Sankey diagram are plotted through
a web browser. I used to have the same problem on my laptop, but switching
from wired network to WiFi fixed the issue.

Any ideas on devel-build solutions? At the moment I switched the plotting
off by using eval=FALSE.

Many thanks,
Vladimir
-- 
http://genat.uk

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Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Vladimir Kiselev

Hi Nitesh,

Many thanks, I will check it in a couple of days.

Cheers,
Vlad

On Mon, 11 Sep 2017, 19:01 Turaga, Nitesh <nitesh.tur...@roswellpark.org>
wrote:

> Hi
>
> Your key will be added in the next run of our script. You can change your
> GitHub keys, our script will take in the new one, and you don’t have to
> resubmit on the google-form.
>
> It is run manually at the moment at noon EST everyday.
>
> Nitesh
> > On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
> >
> > Thanks Simina,
> >
> > I think I've done all the steps described there before and was able to
> push
> > to upstream. I can't do it anymore and try to figure out why.
> >
> > Could anyone else please help?
> >
> > Cheers,
> > Vlad
> >
> > On Mon, 11 Sep 2017, 18:03 Simina Boca <smb...@georgetown.edu> wrote:
> >
> >> Hi, Simina.
> >>
> >> Take a look at the FAQ, #3, here:
> >>
> >> http://bioconductor.org/developers/how-to/git/faq/
> >>
> >> Have you submitted an SSH key somehow?
> >>
> >>
> >>>
> >>> Am I missing something here? Alternatively, I suppose I can just make
> the
> >>> changes I want and simply open another issue, although it would be
> nice to
> >>> have an easy to sync it with what is already on Bioconductor.
> >>>
> >>
> >> When everything is working, you will "own" the bioconductor git repo, so
> >> working it will be roughly equivalent to working with github. Opening an
> >> issue on the package submission repo will not get you what you want and
> is
> >> only for new packages.
> >>
> >> Sean
> >>
> >>
> >> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
> >> vladimir.yu.kise...@gmail.com> wrote:
> >>
> >>> Hi Simina,
> >>>
> >>> Thanks for your quick reply, but it looks like to forgot to paste your
> >>> response from Sean (at least I couldn't find it in your email).
> >>>
> >>> Cheers,
> >>> Vlad
> >>>
> >>> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca <smb...@georgetown.edu>
> >>> wrote:
> >>>
> >>>> Hi Vladimir,
> >>>> This seems like the same error I was getting. Here is the helpful
> advice
> >>>> I got from Sean:
> >>>>
> >>>> Hi, Simina.
> >>>>
> >>>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> >>>> vladimir.yu.kise...@gmail.com> wrote:
> >>>>
> >>>>> Hello,
> >>>>>
> >>>>> I am trying to push a new version of my package to
> git.bioconductor.org.
> >>>>> I
> >>>>> was able to do that in the past. But I've recently changed my public
> key
> >>>>> and not sure whether this causes a problem. However, I can see my new
> >>>>> public key here - https://github.com/wikiselev.keys - and it is the
> >>>>> first
> >>>>> one in the list.
> >>>>>
> >>>>> When I look at the remote I can see git.bioconductor.org there but
> >>>>> when I
> >>>>> try to push to upstream I get an error:
> >>>>>
> >>>>> git remote -v
> >>>>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> >>>>> origin  g...@github.com:hemberg-lab/scmap.git (push)
> >>>>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
> >>>>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
> >>>>>
> >>>>> git push origin master
> >>>>> Everything up-to-date
> >>>>>
> >>>>> git push upstream master
> >>>>> Permission denied (publickey).
> >>>>> fatal: Could not read from remote repository.
> >>>>> Please make sure you have the correct access rights
> >>>>> and the repository exists.
> >>>>>
> >>>>> Could anyone please help?
> >>>>> Many thanks in advance,
> >>>>> Kind regards,
> >>>>> Vladimir
> >>>>>
> >>>> --
> >>>>> http://genat.uk
> >>>>>
> >>>>>[[alternative HTML version deleted]]
> >>>>&g

Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Vladimir Kiselev

Thanks Simina,

I think I've done all the steps described there before and was able to push
to upstream. I can't do it anymore and try to figure out why.

Could anyone else please help?

Cheers,
Vlad

On Mon, 11 Sep 2017, 18:03 Simina Boca <smb...@georgetown.edu> wrote:

> Hi, Simina.
>
> Take a look at the FAQ, #3, here:
>
> http://bioconductor.org/developers/how-to/git/faq/
>
> Have you submitted an SSH key somehow?
>
>
>>
>> Am I missing something here? Alternatively, I suppose I can just make the
>> changes I want and simply open another issue, although it would be nice to
>> have an easy to sync it with what is already on Bioconductor.
>>
>
> When everything is working, you will "own" the bioconductor git repo, so
> working it will be roughly equivalent to working with github. Opening an
> issue on the package submission repo will not get you what you want and is
> only for new packages.
>
> Sean
>
>
> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hi Simina,
>>
>> Thanks for your quick reply, but it looks like to forgot to paste your
>> response from Sean (at least I couldn't find it in your email).
>>
>> Cheers,
>> Vlad
>>
>> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca <smb...@georgetown.edu>
>> wrote:
>>
>>> Hi Vladimir,
>>> This seems like the same error I was getting. Here is the helpful advice
>>> I got from Sean:
>>>
>>> Hi, Simina.
>>>
>>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>>> vladimir.yu.kise...@gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to push a new version of my package to git.bioconductor.org.
>>>> I
>>>> was able to do that in the past. But I've recently changed my public key
>>>> and not sure whether this causes a problem. However, I can see my new
>>>> public key here - https://github.com/wikiselev.keys - and it is the
>>>> first
>>>> one in the list.
>>>>
>>>> When I look at the remote I can see git.bioconductor.org there but
>>>> when I
>>>> try to push to upstream I get an error:
>>>>
>>>> git remote -v
>>>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>>>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>>>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>>>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>>>
>>>> git push origin master
>>>> Everything up-to-date
>>>>
>>>> git push upstream master
>>>> Permission denied (publickey).
>>>> fatal: Could not read from remote repository.
>>>> Please make sure you have the correct access rights
>>>> and the repository exists.
>>>>
>>>> Could anyone please help?
>>>> Many thanks in advance,
>>>> Kind regards,
>>>> Vladimir
>>>>
>>> --
>>>> http://genat.uk
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>>
>>> --
>>> Simina M. Boca
>>> Assistant Professor
>>> Innovation Center for Biomedical Informatics  (ICBI)
>>> Department of Oncology | Georgetown University Medical Center
>>> Department of Biostatistics, Bioinformatics and Biomathematics |
>>> Georgetown University Medical Center
>>> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>>> Center
>>>
>>> 2115 Wisconsin Ave NW, Suite 110
>>> <https://maps.google.com/?q=2115+Wisconsin+Ave+NW,+Suite+110Washington,+DC+20007=gmail=g>
>>> Washington, DC 20007
>>> <https://maps.google.com/?q=2115+Wisconsin+Ave+NW,+Suite+110Washington,+DC+20007=gmail=g>
>>> Phone: (202) 687-1545
>>> Fax: (202) 687-5011
>>> http://icbi.georgetown.edu/boca
>>>
>>>
>>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>>> vladimir.yu.kise...@gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to push a new version of my package to git.bioconductor.org.
>>>> I
>>>> was able to do that in the past. But I'v

Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Vladimir Kiselev

Hi Simina,

Thanks for your quick reply, but it looks like to forgot to paste your
response from Sean (at least I couldn't find it in your email).

Cheers,
Vlad

On Mon, Sep 11, 2017 at 5:58 PM Simina Boca <smb...@georgetown.edu> wrote:

> Hi Vladimir,
> This seems like the same error I was getting. Here is the helpful advice I
> got from Sean:
>
> Hi, Simina.
>
> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to push a new version of my package to git.bioconductor.org.
>> I
>> was able to do that in the past. But I've recently changed my public key
>> and not sure whether this causes a problem. However, I can see my new
>> public key here - https://github.com/wikiselev.keys - and it is the first
>> one in the list.
>>
>> When I look at the remote I can see git.bioconductor.org there but when I
>> try to push to upstream I get an error:
>>
>> git remote -v
>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>
>> git push origin master
>> Everything up-to-date
>>
>> git push upstream master
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights
>> and the repository exists.
>>
>> Could anyone please help?
>> Many thanks in advance,
>> Kind regards,
>> Vladimir
>>
> --
>> http://genat.uk
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Department of Oncology | Georgetown University Medical Center
> Department of Biostatistics, Bioinformatics and Biomathematics |
> Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110
> Washington, DC 20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
>
> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to push a new version of my package to git.bioconductor.org.
>> I
>> was able to do that in the past. But I've recently changed my public key
>> and not sure whether this causes a problem. However, I can see my new
>> public key here - https://github.com/wikiselev.keys - and it is the first
>> one in the list.
>>
>> When I look at the remote I can see git.bioconductor.org there but when I
>> try to push to upstream I get an error:
>>
>> git remote -v
>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>
>> git push origin master
>> Everything up-to-date
>>
>> git push upstream master
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights
>> and the repository exists.
>>
>> Could anyone please help?
>> Many thanks in advance,
>> Kind regards,
>> Vladimir
>>
> --
>> http://genat.uk
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Department of Oncology | Georgetown University Medical Center
> Department of Biostatistics, Bioinformatics and Biomathematics |
> Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110
> Washington, DC 20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
>
-- 
http://genat.uk

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[Bioc-devel] Upstream permission denied

2017-09-11 Thread Vladimir Kiselev

Hello,

I am trying to push a new version of my package to git.bioconductor.org. I
was able to do that in the past. But I've recently changed my public key
and not sure whether this causes a problem. However, I can see my new
public key here - https://github.com/wikiselev.keys - and it is the first
one in the list.

When I look at the remote I can see git.bioconductor.org there but when I
try to push to upstream I get an error:

git remote -v
origin  g...@github.com:hemberg-lab/scmap.git (fetch)
origin  g...@github.com:hemberg-lab/scmap.git (push)
upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
upstreamg...@git.bioconductor.org:packages/scmap.git (push)

git push origin master
Everything up-to-date

git push upstream master
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

Could anyone please help?
Many thanks in advance,
Kind regards,
Vladimir
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Re: [Bioc-devel] git transition for projects with prior git history

2017-07-27 Thread Vladimir Kiselev

Hi Andrew,

I solved it by just adding '--allow-unrelated-histories' to force the merge:
https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories

Cheers,
Vlad

On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew <
andrew_mcda...@urmc.rochester.edu> wrote:

> Is there a recommended recipe to utilize the git.bioconductor.org<
> http://git.bioconductor.org> remote with an existing git repo that has
> non-zero history?  I tried adding the git.bioconductor.org<
> http://git.bioconductor.org> as a remote, making a branch, and then
> checking out a branch on that remote, but it gave my computer sad.  Do I
> need to clone a new repo instead?
>
> Example:
> $ git remote -vv
> bioc https://github.com/Bioconductor-mirror/MAST.git (fetch)
> bioc https://github.com/Bioconductor-mirror/MAST.git (push)
> biocgit 
> g...@git.bioconductor.org:packages/MAST
> (fetch)
> biocgit 
> g...@git.bioconductor.org:packages/MAST
> (push)
> origin g...@github.com:RGLab/MAST.git (fetch)
> origin g...@github.com:RGLab/MAST.git (push
>
> $ git fetch biocgit
> $ git checkout -b bgMaster --track biocgit/master
> ...
> 
> ...
> $ git merge master bgMaster
> fatal: refusing to merge unrelated histories
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] R-3.5.0 devel missing for macOS

2017-06-28 Thread Vladimir Kiselev

Hi,

Seems I can't find the R-3.5.0 devel build for macOS here:
http://r.research.att.com/

Is it ok? Is there any other place I can download it?

Many thanks in advance,
Cheers,
Vlad
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Re: [Bioc-devel] Recommendations for Shiny app on Bioconductor

2017-03-29 Thread Vladimir Kiselev

Hi Wellinton,

As far as I know if you wrap you shiny stuff into an R function that should
be enough. Then you can provide both non-interactive and interactive
functions and the user can choose what to run.

You can have a look at my SC3 package where I implemented a strategy above:
https://github.com/hemberg-lab/SC3

Cheers,
Vlad

On Wed, Mar 29, 2017 at 2:24 PM Welliton Souza  wrote:

> I am developing a web application using Shiny to be distributed as
> Bioconductor package. I would like to know if there are some
> recommendations for better integration with Bioconductor ecosystem.
>
> Best regards,
> Welliton
>
> [[alternative HTML version deleted]]
>
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>
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Re: [Bioc-devel] R version-dependent segfault

2017-01-08 Thread Vladimir Kiselev

Hi Martin,

Great, many thanks for your support and advice. The bug is now fixed for
all the reporters. The solution was simple - I removed both:

#include 
using namespace Rcpp;

from the cpp file and then used Rcpp:: everywhere I needed an Rcpp
function. So that the header at the end looked like this:

#include 
using namespace arma;

For the record, here is a link to this issue on GitHub:
https://github.com/hemberg-lab/SC3/issues/33

Many thanks again,
Cheers,
Vladimir


On Thu, Jan 5, 2017 at 7:32 PM Martin Morgan <martin.mor...@roswellpark.org>
wrote:

> On 01/05/2017 11:10 AM, Vladimir Kiselev wrote:
> > Dear Martin,
> >
> > Many thanks for your reply, it was really helpful. My collaborator ran
> > the commands you suggested and got the following output:
> >
> > *
> > $ Rscript norm_laplacian.R
> > /home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
> >  'norm_laplacian.cpp'
> > g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
> >  -I/home/jake/miniconda3/include
> >  -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
> > -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
> > -I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
> > norm_laplacian.cpp -o norm_laplacian.o
> > g++ -shared -L/home/jake/miniconda3/lib/R/lib
> > -L/home/jake/miniconda3/lib -lgfortran -o sourceCpp_2.so
> > norm_laplacian.o -L/home/jake/miniconda3/lib/R/lib -lRlapack
> > -L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
> > -L/home/jake/miniconda3/lib/R/lib -lR
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 16.10
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> >  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics  grDevices utils datasets  base
> >
> > other attached packages:
> > [1] Rcpp_0.12.8
> >
> > loaded via a namespace (and not attached):
> > [1] tools_3.3.2   RcppArmadillo_0.7.600.1.0
> >
> > $ g++ --version|head -n1
> > g++ (Ubuntu 6.2.0-5ubuntu12) 6.2.0 20161005
> > *
> >
> > So running the simplified code did not produce a segfault and suggested
> > that the problem was in SC3::norm_laplacian(). And indeed, running
> > valgrind with SC3::norm_laplacian(matrix(runif(100), nrow = 10)) did
> > catch the error:
> >
> > *
> > $ R -d valgrind -f norm_laplacian.R
> > ==7046== Memcheck, a memory error detector
> > ==7046== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
> > ==7046== Using Valgrind-3.12.0.SVN and LibVEX; rerun with -h for
> > copyright info
> > ==7046== Command: /home/jake/miniconda3/lib/R/bin/exec/R -f
> norm_laplacian.R
> > ==7046==
> >
> > R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
> > Copyright (C) 2016 The R Foundation for Statistical Computing
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> >> library(Rcpp)
> >> sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
> > /home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
> >  'norm_laplacian.cpp'
> > g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
> >  -I/home/jake/miniconda3/include
> >  -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
> > -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
> > -I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
> > norm_laplacian.cpp -o norm_laplacian.o
> > g++ -shared -L/home/jake/miniconda3/lib/R/lib
> > -L/home/jake/miniconda3/lib -lgfortran -o sourceCpp_2.so
> > norm_laplacian.o -L/home/jake/miniconda3/lib/R/lib -lRlapack
> > -L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
> > -L/home/jake/miniconda3/lib/R/lib -lR
> >> xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> >> SC3::norm_laplacian(matrix(runif(100), nrow = 10))
> > ==7046== Use of uninitialised value of size 8
> > ==7046==at 0x213645B8: direct_max (op_max_meat.hpp:362)
> > ==7046==by 0x213645B8: max (Mat_meat.hpp:6801)
> > ==7046==by 0x213645B8: norm_laplacian(arma::Mat)
> > (cppFunctions.cpp:87)
> > ==7046==by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)

Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

2017-01-05 Thread Vladimir Kiselev

Maybe 1.0.4 is smaller than 1.0.30? Try to change to 1.0.31.

On Fri, 6 Jan 2017, 05:32 Anand MT,  wrote:

> Hi Vincent,
>
> Thanks for reply. I swear this was OK till yesterday for updated version!
> This "file not found" issue often occurs but it resolves by itself during
> next builds. Anyways, even when everything was OK, package didn't update to
> newer version.
>
>
>
> 
> From: Vincent Carey 
> Sent: 06 January 2017 08:27:01
> To: Anand MT
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] maftools package not updated after pushing bug
> fixes.
>
>
>
> On Thu, Jan 5, 2017 at 9:33 PM, Anand MT > wrote:
> Hi,
>
>
> I recently pushed few bug fixes and removed some dependency packages which
> were no longer required. I did this a week ago and updated version to 1.0.4
> from 1.0.30.
>
> Build reports are OK for updated version.
>
> http://bioconductor.org/checkResults/release/bioc-LATEST/maftools/
>
> Hi -- there is an error for linux build on that link.
>
>
>
>
> However, release site is still at older 1.0.30. How to proceed now ?
>
> Probably have to fix the build error --
>
>
> Done !
> Quitting from lines 152-153 (maftools.Rmd)
> Error: processing vignette 'maftools.Rmd' failed with diagnostics:
> file not found: /dev/shm/file6fd4ebc7d82
>
> Execution halted
>
>
>
>
> Thank you.
>
> -Anand
>
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>
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Re: [Bioc-devel] R version-dependent segfault

2017-01-05 Thread Vladimir Kiselev

 Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5268B8C: Rf_applyClosure (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267BBF: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6C1E: Rf_ReplIteration (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6DD1: R_ReplConsole (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A8758: run_Rmainloop (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==  Address 0xa000a is not stack'd, malloc'd or (recently) free'd
==7046==

 *** caught segfault ***
address 0xa000a, cause 'memory not mapped'

Traceback:
 1: .Call("SC3_norm_laplacian", PACKAGE = "SC3", A)
 2: SC3::norm_laplacian(matrix(runif(100), nrow = 10))
An irrecoverable exception occurred. R is aborting now ...
==7046==
==7046== Process terminating with default action of signal 11 (SIGSEGV)
==7046==at 0x5C4C4DD: raise (raise.c:53)
==7046==by 0x52A76C4: sigactionSegv (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5C4C62F: ??? (in /lib/x86_64-linux-gnu/libpthread-2.24.so)
==7046==by 0x213645B7: direct_max (op_max_meat.hpp:360)
==7046==by 0x213645B7: max (Mat_meat.hpp:6801)
==7046==by 0x213645B7: norm_laplacian(arma::Mat)
(cppFunctions.cpp:87)
==7046==
==7046== HEAP SUMMARY:
==7046== in use at exit: 149,681,035 bytes in 81,447 blocks
==7046==   total heap usage: 275,293 allocs, 193,846 frees, 410,601,938
bytes allocated
==7046==
==7046== LEAK SUMMARY:
==7046==definitely lost: 0 bytes in 0 blocks
==7046==indirectly lost: 0 bytes in 0 blocks
==7046==  possibly lost: 0 bytes in 0 blocks
==7046==still reachable: 149,681,035 bytes in 81,447 blocks
==7046==   of which reachable via heuristic:
==7046== newarray   : 7,152 bytes in 1
blocks
==7046== suppressed: 0 bytes in 0 blocks
==7046== Rerun with --leak-check=full to see details of leaked memory
==7046==
==7046== For counts of detected and suppressed errors, rerun with: -v
==7046== Use --track-origins=yes to see where uninitialised values come from
==7046== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)
*

So, it looks like the problem is in finding the max of the input matrix A,
specifically in the direct_max() function of Armadillo library. But the
segfault only appears when running SC3::norm_laplacian() and not the
simplified code. Does it suggest that I have some linking or exporting
problems in the package? Can you think of any solution to this problem?

In case this can help, the SC3::norm_laplacian() function is stored in the
file with the following header:

#include 
#include 
using namespace arma;
using namespace Rcpp;


Many thanks in advance,
Kind regards,
Vladimir

On Thu, Jan 5, 2017 at 12:19 PM Martin Morgan <martin.mor...@roswellpark.org>
wrote:

> On 01/05/2017 06:41 AM, Vladimir Kiselev wrote:
> > My package (SC3 -
> http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
> > has a function that causes R version/platform-dependent seqfault. Here is
> > the function (it's in C++ using RccpArmadillo):
> >
> > arma::mat norm_laplacian(arma::mat A) {
> > A = exp(-A/A.max());
> > arma::rowvec D_row = pow(sum(A), -0.5);
> > A.each_row() %= D_row;
> > colvec D_col = conv_to< colvec >::from(D_row);
> > A.each_col() %= D_col;
> > arma::mat res = eye(A.n_cols, A.n_cols) - A;
> > return(res);
> > }
> >
> > The test code that provides a segfault on some R versions/platforms:
> > SC3::norm_laplacian(matrix(runif(100), nrow = 10))
>
> The first line of attack is to simplify the problem as much as possible.
> I did this by writing a C++ file norm_laplacian.cpp
>
> #include 
>
> using namespace arma;
>
> // [[Rcpp::depends(RcppArmadillo)]]
>
> // [[Rcpp::export]]
> arma::mat norm_laplacian(arma::mat A) {
>  A = exp(-A/A.max());
>  arma::rowvec D_row = pow(sum(A), -0.5);
>  A.each_row() %= D_row;
>  colvec D_col = conv_to< colvec >::from(D_row);
>  A.each_col() %= D_col;
>  arma::mat res = eye(A.n_cols, A.n_cols) - A;
>  return(res);
> }
>
> and then in R, e.g., norm_laplacian.R
>
>  library(Rcpp)
>  sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
>  xx <- norm_laplacian(matrix(runif(100), nrow = 10))
>  sessionInfo()
>
> It would be helpful to use set.seed() to make the example more
> reproducible. One would hope that
>
>  R -f norm_laplacian.R
>
> would produce a segfault. Unfortunately not for me. My next step was to
> run this code under valgrind to look for invalid memory access
>
>  R -d valgrind -f norm_laplacian.R
>
> again hoping for a report of 'invalid wri

Re: [Bioc-devel] Which platform are the vignettes built on?

2017-01-05 Thread Vladimir Kiselev

Great, many thanks Martin!

On Thu, Jan 5, 2017 at 11:22 AM Martin Morgan <martin.mor...@roswellpark.org>
wrote:

> On 01/05/2017 06:16 AM, Vladimir Kiselev wrote:
> > Dear All,
> >
> > After pushing a new version of a package to bioc-devel the vignettes are
> > rebuilt, but I cannot find on which platform they were built on. Is it
> > linux, windows or mac?
>
> They are built on all platforms as part of the build / check cycle. The
> vignettes made available on the web site are from the linux builds.
>
> Martin
>
> >
> > Thanks,
> > Vladimir
> >
>
>
> This email message may contain legally 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
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> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
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[Bioc-devel] R version-dependent segfault

2017-01-05 Thread Vladimir Kiselev

My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):

arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A), -0.5);
A.each_row() %= D_row;
colvec D_col = conv_to< colvec >::from(D_row);
A.each_col() %= D_col;
arma::mat res = eye(A.n_cols, A.n_cols) - A;
return(res);
}

The test code that provides a segfault on some R versions/platforms:
SC3::norm_laplacian(matrix(runif(100), nrow = 10))

The segfault usually looks like this:
*** caught segfault ***
address 0x7ffdc981e000, cause 'memory not mapped'

(where address can be a different sequence)

So far by a collaborative effort (me and some users of the package) we
figured out configurations that cause or do not cause a segfault:

* Configurations causing a segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

* Configurations causing no segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

R Under development (unstable) (2016-10-20 r71540)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

More details on our discussion can be found here:
https://github.com/hemberg-lab/SC3/issues/33

Has anybody had a similar issue? Do you have any suggestions on how to fix
this, except rewriting the function in R? Or maybe there already exists a
normalised Laplacian function written in C++?

Many thanks,
Cheers,
Vladimir
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[Bioc-devel] Which platform are the vignettes built on?

2017-01-05 Thread Vladimir Kiselev

Dear All,

After pushing a new version of a package to bioc-devel the vignettes are
rebuilt, but I cannot find on which platform they were built on. Is it
linux, windows or mac?

Thanks,
Vladimir
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Re: [Bioc-devel] there is no package called ‘BiocStyle’

[Bioc-devel] there is no package called ‘BiocStyle’

[Bioc-devel] Undefined slot classes warning

Re: [Bioc-devel] Pandoc issues

[Bioc-devel] TLS error in vignette on all devel builds

Re: [Bioc-devel] Upstream permission denied

Re: [Bioc-devel] Upstream permission denied

Re: [Bioc-devel] Upstream permission denied

[Bioc-devel] Upstream permission denied

Re: [Bioc-devel] git transition for projects with prior git history

[Bioc-devel] R-3.5.0 devel missing for macOS

Re: [Bioc-devel] Recommendations for Shiny app on Bioconductor

Re: [Bioc-devel] R version-dependent segfault

Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

Re: [Bioc-devel] R version-dependent segfault

Re: [Bioc-devel] Which platform are the vignettes built on?

[Bioc-devel] R version-dependent segfault

[Bioc-devel] Which platform are the vignettes built on?

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