Re: [Bioc-devel] Using https to maintain a package
On Tue, May 8, 2018 at 12:34 AM Monther Alhamdoosh wrote: > Hi, > > Is there a way to access Bioconductor git repository via https instead of > ssh? > Just for read-only access. Write access requires ssh. Sean > > Thanks, > Monther > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Using https to maintain a package
Hi, Sean is correct. There is only read-only access available through HTTP. You would need SSH access for read-write privileges at the moment. We show this in the package landing pages. As you scroll to “Package Archives”, you will notice 'Source repository’, and 'Source Repository (Developer Access)' Take the package “BiocParallel” for example: https://bioconductor.org/packages/release/bioc/html/BiocParallel.html Source Repository: git clone https://git.bioconductor.org/packages/BiocParallel Source Repository (Developer Access): git clone g...@git.bioconductor.org:packages/BiocParallel Best, Nitesh > On May 8, 2018, at 6:17 AM, Sean Davis wrote: > > On Tue, May 8, 2018 at 12:34 AM Monther Alhamdoosh > wrote: > >> Hi, >> >> Is there a way to access Bioconductor git repository via https instead of >> ssh? >> > > Just for read-only access. Write access requires ssh. > > Sean > > >> >> Thanks, >> Monther >> >>[[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > -- > Sean Davis, MD, PhD > Center for Cancer Research > National Cancer Institute > National Institutes of Health > Bethesda, MD 20892 > https://seandavi.github.io/ > https://twitter.com/seandavis12 > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel 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 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 by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] proc.time error
On 05/08/2018 02:58 AM, Anand MT wrote:
Hi Developers,
I maintain Bioconductor package maftools, which has been failing to build on
WIndows platform since it the new release. Error seems to be originating while
running examples with the below error.
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
The current build report shows release failing on 32-bit windows
http://bioconductor.org/checkResults/3.7/bioc-LATEST/maftools/tokay2-checksrc.html
because the example is too large. The solution, and better practice, is
to use more modest computation in the example.
...
> seg = system.file('extdata', 'TCGA.AB.3009.hg19.seg.txt', package =
'maftools')
> TCGA.AB.3009.clust <- inferHeterogeneity(maf = laml, tsb =
'TCGA-AB-3009',
+ segFile = seg, vafCol = 'i_TumorVAF_WU')
Processing TCGA-AB-3009..
Error: cannot allocate vector of size 1.3 Gb
Execution halted
The devel build report
http://bioconductor.org/checkResults/3.8/bioc-LATEST/maftools/malbec1-buildsrc.html
shows all builds failing because of use of an undefined object in the
vignette; this would appear to be a programming error.
Quitting from lines 269-270 (maftools.Rmd)
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
object 'Cytoband' not found
Execution halted
Martin
I have googled the issue, many answers suggests to include examples within
/dontrun{} to avoid errors. But this has never been the issue before and
package has built successfully with the same examples. How do I solve this ?
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Re: [Bioc-devel] class name collision in cache: igvR and Gviz
Thanks Paul.
I've made improvements to the methods package so that there will no longer
be any messages about AnnotationTrack being duplicated, but I'll need to
work through some failures this is causing in tests.
The first issue is interesting though. Since Gviz defines an initialize()
for AnnotationTrack, dispatch ends up using that intsead of the default.
That method (incorrectly in my opinion) silently drops unrecognized
arguments in "..." so it is effectively a no-op. Ideally the method would
eventually call callNextMethod(). Not doing so makes assumptions about how
the parent object is initialized. It would also make this case work, just
by luck. This is one reason why defining initialize() methods is tricky and
should be avoided.
Unfortunately, the methods package will dispatch to a method, regardless of
the package of origin, unless there are methods with signatures containing
two or more classes of the same name. This might be easy to fix but there
could be performance regressions. This problem will happen all the time if
there are initialize() methods around. You should be able to avoid this
just by defining your own initialize() method that just calls the next
method. Ideally though Gviz would just drop its one.
Michael
On Mon, May 7, 2018 at 11:14 AM, Paul Shannon <
paul.thurmond.shan...@gmail.com> wrote:
> Hi Michael,
>
> > On May 4, 2018, at 1:36 PM, Michael Lawrence
> wrote:
> >
> > Do you have a reproducible example of this? It's probably a bug in the
> methods package.
> >
>
> Sorry I did not get to this sooner. Here are two symptoms of the cache
> class name collision:
>
>1) igvR::displayTrack, if called after motifbreakR::plotMB, fails (see
> error message below)
>2) plotMB, if called after igvR is loaded, reports the class name
> collision.
>
> - Paul
>
> library(SNPlocs.Hsapiens.dbSNP150.GRCh38)
> library(BSgenome.Hsapiens.UCSC.hg38)
> library(motifbreakR)
>
> snp <- "rs12050029"
>
> snps.gr <- snps.from.rsid(rsid = snp,
> dbSNP=SNPlocs.Hsapiens.dbSNP150.GRCh38,
> search.genome=BSgenome.Hsapiens.UCSC.hg38)
>
>
> results <- motifbreakR(snpList = snps.gr, filterp = TRUE,
>pwmList = query(MotifDb, "jaspar2018"),
>threshold = 1e-4,
>method = "ic",
>bkg = c(A=0.25, C=0.25, G=0.25, T=0.25),
>BPPARAM = BiocParallel::bpparam("SerialParam"))
>
> plotMB(results = results, rsid = snp, effect = c("weak", "strong"))
>
>
> library(igvR)
> igv <- igvR()
> setGenome(igv, "hg38")
> snp.track <- GRangesAnnotationTrack("snp", snps.gr, color="red")
> displayTrack(igv, snp.track)
>
># this error is only seen if motifbreakR - and thus Gviz - have been
> loaded
># otherwise, displayTrack works fine
># Error in if (trackType == "variant" && source == "file" && fileFormat
> == :
># missing value where TRUE/FALSE
>
> plotMB(results = results, rsid = snp, effect = c("weak", "strong"))
>
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
># Found more than one class "AnnotationTrack" in cache; using the
> first, from namespace 'Gviz'
># Also defined by 'igvR'
>
>
>
>
>
> > Michael
> >
> > On Fri, May 4, 2018 at 10:52 AM, Paul Shannon <
> paul.thurmond.shan...@gmail.com> wrote:
> > I just discovered a class name collision - AnnotationTrack, in Gviz and
> my new package igvR. wish to get wise counsel before proceeding with a
> fix. Here’s the error message:
> >
> >Found more than one class "AnnotationTrack" in cache;
> >using the first, from namespace ‘igvR' Also defined by ‘Gviz’
> >
> > AnnotationTrack is an abstract base class in my new package igvR. The
> concrete derived classes at present are
> >
> > DataFrameAnnotationTrack
> > GRangesAnnotationTrack
> > UCSCBedAnnotationTrack
> >
> > It would be easy for me to rename AnnotationTrack to
> “GenomeAnnotationTrack” or even “igvAnnotationTrack”, thereby avoiding the
> name clash.
> >
> > Reasonable? Fix in both release and devel?
> >
> > Thanks -
> >
> > - Paul
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
>
>
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Re: [Bioc-devel] Using https to maintain a package
Thanks for the info, both. Cheers, Monther On Tue, May 8, 2018 at 9:42 PM Turaga, Nitesh wrote: > Hi, > > Sean is correct. There is only read-only access available through HTTP. > You would need SSH access for read-write privileges at the moment. > > We show this in the package landing pages. As you scroll to “Package > Archives”, you will notice 'Source repository’, and 'Source Repository > (Developer Access)' > > Take the package “BiocParallel” for example: > > > https://bioconductor.org/packages/release/bioc/html/BiocParallel.html > > > Source Repository: git clone > https://git.bioconductor.org/packages/BiocParallel > Source Repository (Developer Access): git clone > g...@git.bioconductor.org:packages/BiocParallel > > Best, > > Nitesh > > > On May 8, 2018, at 6:17 AM, Sean Davis wrote: > > > > On Tue, May 8, 2018 at 12:34 AM Monther Alhamdoosh > > > wrote: > > > >> Hi, > >> > >> Is there a way to access Bioconductor git repository via https instead > of > >> ssh? > >> > > > > Just for read-only access. Write access requires ssh. > > > > Sean > > > > > >> > >> Thanks, > >> Monther > >> > >>[[alternative HTML version deleted]] > >> > >> ___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > -- > > Sean Davis, MD, PhD > > Center for Cancer Research > > National Cancer Institute > > National Institutes of Health > > Bethesda, MD 20892 > > https://seandavi.github.io/ > > https://twitter.com/seandavis12 > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > 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 > 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 by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17
Dear Martin Morgan,
Thank you Morgan for informing me to join your annual conference BioC 2018.
I am very much interested to attend the BioC 2018 conference .
Presently I am perusing my PhD from CSIR-Indian Institute of Chemical
biology.
So it is not possible to collect all the money to pay all the expenses
myself.
I would like to know if I am selected for the scholarship, they will
pay for costs
such as
travel, accommodation, and registration ? Or they will pay only $500 per
person?
If it is possible please send me an invitation letter for the annual
conference BioC 2018.
The invitation letter will help me for grant application to the indian
funding body such as DBT or CSIR etc.
Thank you
regards
Pijush
On Mon, May 7, 2018 at 2:59 AM, Martin Morgan wrote:
> Join us for our annual conference BioC 2018: Where Software and Biology
> Connect, at Victoria University on the University of Toronto campus
>
> http://bioc2018.bioconductor.org
>
> The deadline for poster, talk, scholarship (travel, accommodation, and
> registration), and workshop applications is May 17, see
>
> http://bioc2018.bioconductor.org/call-for-abstracts
> http://bioc2018.bioconductor.org/scholarships
>
> Martin Morgan
> Bioconductor
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
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>
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