Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Michael Lawrence via Bioc-devel
Good call. Didn't know about seqlevelsInUse(). On Wed, Sep 11, 2019 at 8:29 AM Pages, Herve wrote: > > Or more accurately: > >as(seqinfo(bsgenome)[seqlevelsInUse(grl)], "GRanges") > > since not all seqlevels are necessarily "in use" (i.e. not necessarily > represented in seqnames(grl)). > >

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

2019-09-11 Thread Vincent Carey
I seem to be running into a similar problem with BiocOncoTK on windows The build report for tokay1 shows: Loading required package: ontologyIndex Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Bhagwat, Aditya
Hi Herve, > It feels that a coercion method from BSgenome to GRanges should rather be > defined in the BSgenome package itself. :-) > Patch/PR welcome on GitHub. Owkies. What pull/fork/check/branch protocol to be followed? > Is this what you have in mind for this coercion? >

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Pages, Herve
Hi Aditya, On 9/11/19 01:31, Bhagwat, Aditya wrote: > Hi Herve, > > > > It feels that a coercion method from BSgenome to GRanges should > rather be defined in the BSgenome package itself. > > :-) > > > > Patch/PR welcome on GitHub. > > Owkies. What pull/fork/check/branch protocol to be

Re: [Bioc-devel] Reset to a previous commit

2019-09-11 Thread Simon Dirmeier
Hello, thanks Nitesh. I reverted the commits accordingly. Cheers, Simon On 10.09.19 16:45, Turaga, Nitesh wrote: Hi Simon, I take this back actually. I think the best way forward is just undo the code changes, and add a new version number to it ( 1.9.3) and push. Step 1, Since

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Bhagwat, Aditya
Hi Herve, Thank you for your responses. >From your response, it is clear that the vcountPDict use case does not need a >BSgenome -> GRanges coercer. The karyoploteR use case still requires it, though, to allow plotting of only the chromosomal BSgenome portions: chromranges <-

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

2019-09-11 Thread Pages, Herve
On 9/11/19 00:50, Vincent Carey wrote: > I seem to be running into a similar problem with BiocOncoTK on windows > > The build report for tokay1 shows: > > Loading required package: ontologyIndex > Invalid Parameter - /figure-html > Warning in shell(paste(c(cmd, args), collapse = " ")) : >

[Bioc-devel] new package for accessing some chemical and biological databases

2019-09-11 Thread Pierrick Roger
Dear all, I'd like to submit by package biodb (https://github.com/pkrog/biodb) in the near future. The aim of this package is to present a unified access to diverse databases (ChEBI, KEGG databases, Uniprot, ...). For running examples, building vignettes and running tests, I use a cache that is

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

2019-09-11 Thread Kasper Daniel Hansen
Yeah, does this imply that the render operation uses (or tries to use) ImageMagick? That's news to me, but I am not following this closely. On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve wrote: > On 9/11/19 00:50, Vincent Carey wrote: > > I seem to be running into a similar problem with

Re: [Bioc-devel] RGL warning

2019-09-11 Thread Kasper Daniel Hansen
GLX is a module for X11. You need that module installed in whatever X11 installation you have. My understanding (which is weak) is that GLX is a standard module so it is weird it is missing. On Tue, Sep 10, 2019 at 12:39 PM Zhezhen Wang wrote: > Hi > > I am having the following warnings and not

Re: [Bioc-devel] new package for accessing some chemical and biological databases

2019-09-11 Thread Shepherd, Lori
No we do not allow such submodules currently in Bioconductor. How big is the object? I assume putting the data object in the package increases the package size over the limit? If this is the case, We would recommend storing the data in the ExperimentHub. See [Creating An ExperimentHub

Re: [Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

2019-09-11 Thread Bhagwat, Aditya
Oh, that's pretty cool :-) I knew I was overlooking something! Thanks Lori Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Wednesday, September 11, 2019 2:54 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: Collapsing a GRangesList

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Michael Lawrence via Bioc-devel
I'm pretty surprised that the karyoploteR package does not accept a Seqinfo since it is plotting chromosomes. But again, please consider just doing as(seqinfo(bsgenome), "GRanges"). On Wed, Sep 11, 2019 at 3:59 AM Bhagwat, Aditya wrote: > > Hi Herve, > > Thank you for your responses. > From your

[Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

2019-09-11 Thread Bhagwat, Aditya
Dear bioc-devel, When using unlist to collapse a GRangesList into a GRanges one looses names(GRangesList). Since I need a name-preserving collapser, I defined the following in multicrispr. My

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Bhagwat, Aditya
Thanks Michael, The important detail is that I want to plot the relevant chromosomes only relevant_chromosomes <- GenomeInfoDb::seqnames(grangeslist) %>% S4Vectors::runValue() %>% Reduce(union, .) %>%

Re: [Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

2019-09-11 Thread Shepherd, Lori
In what way are you feeling they loose names? > grlist <- GenomicRanges::GRangesList( gr1 = GenomicRanges::GRanges('chr1', > '1-100', strand = '-'), gr2 = GenomicRanges::GRanges('chr1', '101-200', > strand = '-')) > names(grlist) [1] "gr1" "gr2" > temp = unlist(grlist) > names(temp) [1]

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Michael Lawrence via Bioc-devel
So why not just do: as(seqinfo(bsgenome)[unique(unlist(seqnames(grl)))], "GRanges") Michael On Wed, Sep 11, 2019 at 5:55 AM Bhagwat, Aditya wrote: > > Thanks Michael, > > The important detail is that I want to plot the relevant chromosomes only > > relevant_chromosomes <-

Re: [Bioc-devel] RGL warning

2019-09-11 Thread Zhezhen Wang
Thanks, do we need to solve all the warnings? Zhezhen From: Kasper Daniel Hansen Sent: Wednesday, September 11, 2019 8:12 AM To: Zhezhen Wang Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] RGL warning GLX is a module for X11. You need that module

[Bioc-devel] Troubles with Windows build

2019-09-11 Thread Ulrich Bodenhofer
Dear colleagues, I have two issues with the Windows BUILD BIN of our 'msa' package. (to my horror, I figured out that the first problem has existed for quite a while; I am deeply sorry for that!) The main problem can be seen on

Re: [Bioc-devel] Troubles with Windows build

2019-09-11 Thread Pages, Herve
Hi Ulrich, On 9/11/19 07:38, Ulrich Bodenhofer wrote: > Dear colleagues, > > I have two issues with the Windows BUILD BIN of our 'msa' package. (to > my horror, I figured out that the first problem has existed for quite a > while; I am deeply sorry for that!) > > The main problem can be seen

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Pages, Herve
Or more accurately: as(seqinfo(bsgenome)[seqlevelsInUse(grl)], "GRanges") since not all seqlevels are necessarily "in use" (i.e. not necessarily represented in seqnames(grl)). H. On 9/11/19 08:26, Hervé Pagès wrote: > The unique seqnames is what we call the seqlevels. So just: > >  

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

2019-09-11 Thread Pages, Herve
The unique seqnames is what we call the seqlevels. So just: as(seqinfo(bsgenome)[seqlevels(grl)], "GRanges") H. On 9/11/19 07:42, Michael Lawrence wrote: > So why not just do: > > as(seqinfo(bsgenome)[unique(unlist(seqnames(grl)))], "GRanges") > > Michael > > On Wed, Sep 11, 2019 at 5:55

Re: [Bioc-devel] RGL warning

2019-09-11 Thread Shepherd, Lori
Ideally yes all ERROR/WARNING/NOTES should be cleaned up. Depending on the NOTES/WARNINGS some may be out of your control. You could open a discussion with your reviewer on your open submission for BioTIP to see if there could be an exception or what else could be done about it.

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

2019-09-11 Thread Pages, Herve
New to me too. But it seems that knitr suggests magick, which itself has SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb) Don't know when this knitr dep on magick was introduced tough... Bummer! H. On 9/11/19 06:13, Kasper Daniel Hansen wrote: > Yeah,

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th September

2019-09-11 Thread Mike Smith
Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 19th September at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/645510122?src=join_info (Meeting ID: 645 510 122) More details can be found in