Re: [Bioc-devel] Error with InteractionSet package
The randomness of the errors is concerning, especially given that none of these functions should be calling compiled code yet. Can you produce a minimal working example that reproducibly triggers at least one of the errors? And post your session information. -Aaron On 08/11/16 17:34, Ioannis Vardaxis wrote: Hi, I am trying to combine two GRanges from two anchors of same length in to a Gitnteractions object and I get the following error: PairedData=InteractionSet::GInteractions(anchor1=Anchor1,anchor2=Anchor2) Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, : first and second anchor vectors have different lengths length(Anchor1) [1] 33705839 length(Anchor2) [1] 33705839 traceback() 5: stop(msg) 4: .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, metadata = metadata, mode = mode) 3: .local(anchor1, anchor2, regions, ...) 2: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2) 1: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2) While they clearly have the same length. If I then run it again it works fine. If I then run again one more time I get: Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, : all anchor indices must be finite integers In addition: Warning message: In new.pos[o] <- new.pos : number of items to replace is not a multiple of replacement length I run it again and I get the correct results. It seems like it is quite random if I get en error or not. -- Ioannis Vardaxis Stipendiat IMF NTNU [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats
This is a bit embarrassing. Somehow I was convinced it was December. All
looks fine.("... you have gained a level in Distracted Professorship").
Kasper
On Tue, Nov 8, 2016 at 11:50 AM, Hervé Pagès wrote:
> Hi Kasper,
>
> The download stats just got updated:
>
> http://bioconductor.org/packages/stats/
>
> They are updated twice a week, on Tuesday and Friday between 8
> and 9 AM PST. Note that because of how the download log files are
> generated and propagated to the machine where the stats are computed,
> and because of the time it takes to generate the stats reports for
> all the packages, the current stats don't take into account the
> downloads that happened during the last 24 hours (more or less).
>
> Cheers,
> H.
>
>
> On 11/08/2016 07:50 AM, Kasper Daniel Hansen wrote:
>
>> It was pointed out to me that the (sub) heading on the page tells me that
>> the script for counting downloads was last run Nov 4th, explaining the
>> discrepancy.
>>
>> On Tue, Nov 8, 2016 at 9:24 AM, Kasper Daniel Hansen <
>> kasperdanielhan...@gmail.com> wrote:
>>
>> Is there something wrong with the download stats in November. All the
>>> packages I look at have lost about 85-90% compared to other months of the
>>> year:
>>> http://bioconductor.org/packages/stats/bioc/GenomicRanges/
>>>
>>> Best,
>>> Kasper
>>>
>>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
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>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax:(206) 667-1319
>
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[Bioc-devel] Error with InteractionSet package
Hi, I am trying to combine two GRanges from two anchors of same length in to a Gitnteractions object and I get the following error: > PairedData=InteractionSet::GInteractions(anchor1=Anchor1,anchor2=Anchor2) Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, : first and second anchor vectors have different lengths > length(Anchor1) [1] 33705839 > length(Anchor2) [1] 33705839 > traceback() 5: stop(msg) 4: .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, metadata = metadata, mode = mode) 3: .local(anchor1, anchor2, regions, ...) 2: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2) 1: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2) While they clearly have the same length. If I then run it again it works fine. If I then run again one more time I get: Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions, : all anchor indices must be finite integers In addition: Warning message: In new.pos[o] <- new.pos : number of items to replace is not a multiple of replacement length I run it again and I get the correct results. It seems like it is quite random if I get en error or not. -- Ioannis Vardaxis Stipendiat IMF NTNU [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats
Hi Kasper, The download stats just got updated: http://bioconductor.org/packages/stats/ They are updated twice a week, on Tuesday and Friday between 8 and 9 AM PST. Note that because of how the download log files are generated and propagated to the machine where the stats are computed, and because of the time it takes to generate the stats reports for all the packages, the current stats don't take into account the downloads that happened during the last 24 hours (more or less). Cheers, H. On 11/08/2016 07:50 AM, Kasper Daniel Hansen wrote: It was pointed out to me that the (sub) heading on the page tells me that the script for counting downloads was last run Nov 4th, explaining the discrepancy. On Tue, Nov 8, 2016 at 9:24 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: Is there something wrong with the download stats in November. All the packages I look at have lost about 85-90% compared to other months of the year: http://bioconductor.org/packages/stats/bioc/GenomicRanges/ Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats
It was pointed out to me that the (sub) heading on the page tells me that the script for counting downloads was last run Nov 4th, explaining the discrepancy. On Tue, Nov 8, 2016 at 9:24 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > Is there something wrong with the download stats in November. All the > packages I look at have lost about 85-90% compared to other months of the > year: > http://bioconductor.org/packages/stats/bioc/GenomicRanges/ > > Best, > Kasper > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Availability shield URLs
Awesome, thanks Dan! On Tue, Nov 8, 2016 at 9:40 AM, Martin Morgan wrote: > On 11/02/2016 11:54 AM, Leonardo Collado Torres wrote: > >> Hi, >> >> I'm just curious why >> http://www.bioconductor.org/shields/availability/release/derfinder.svg >> works but http://www.bioconductor.org/shields/availability/release/rec >> ount.svg >> doesn't (http://www.bioconductor.org/shields/availability/3.4/recount.svg >> does work). The same is true for devel. >> >> derfinder has been around longer than recount, so that might be it. I >> don't think that it's an alphabetical issue since >> http://www.bioconductor.org/shields/availability/release/regionReport.svg >> does work. >> >> This is a very minor thing. It's just easier to simply use >> release/devel instead of 3.4/3.5 and changing it every cycle. >> > > These are back to functioning now, thanks to some detective work from Dan. > Thanks for the report. Martin > > >> Best, >> Leo >> >> ___ >> 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] Availability shield URLs
On 11/02/2016 11:54 AM, Leonardo Collado Torres wrote:
Hi,
I'm just curious why
http://www.bioconductor.org/shields/availability/release/derfinder.svg
works but http://www.bioconductor.org/shields/availability/release/recount.svg
doesn't (http://www.bioconductor.org/shields/availability/3.4/recount.svg
does work). The same is true for devel.
derfinder has been around longer than recount, so that might be it. I
don't think that it's an alphabetical issue since
http://www.bioconductor.org/shields/availability/release/regionReport.svg
does work.
This is a very minor thing. It's just easier to simply use
release/devel instead of 3.4/3.5 and changing it every cycle.
These are back to functioning now, thanks to some detective work from
Dan. Thanks for the report. Martin
Best,
Leo
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[Bioc-devel] download stats
Is there something wrong with the download stats in November. All the packages I look at have lost about 85-90% compared to other months of the year: http://bioconductor.org/packages/stats/bioc/GenomicRanges/ Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Question about sumbition process and biocviews
Create a folder \inst and place the REFERENCES.bib in it. (see attached)
Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}.
You have to have the Rdpack installed.
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 07/11/16 13:49, "Ioannis Vardaxis"
wrote:
>
>
>
>
>
>On 07/11/16 13:43, "Martin Morgan" wrote:
>
>>On 11/07/2016 07:35 AM, Ioannis Vardaxis wrote:
>>> Ok,
>>>
>>> Consider an R.script with a function and roxygen entries above the
>>> function out the author etc. One of the entries there is the following:
>>>#'
>>> @references \insertRef{key}{pkg}.
>>> This macro is given by the Rdpack R package for using references in the
>>> help pages. Where I have created a REFERENCES.bib file placed in the
>>>/inst
>>> folder containing the references I want to use.
>>> ³key² is the references key from the bib file and ³pkg² is my package
>>>name.
>>
>>what minimal changes do I need to make to this package to be able to
>>reproduce the warnings below?
>>
>>https://github.com/mtmorgan/PkgA/tree/parse-Rd-insertRef
>>
>>Martin
>>
>>>
>>> Roxygen produces the expected output when I use the above macro.
>>>
>>> Now when I run:
>>> system("R CMD build pkg²)#runs ok
>>> system("R CMD BiocCheck pkg_0.99.0.tar.gz²)# gives the following :
>>>
>>> * This is BiocCheck, version 1.11.0.
>>> * BiocCheck is a work in progress. Output and severity of issues may
>>> change.
>>> * Installing package...
>>> * Checking for version number mismatch...
>>> * Checking vignette directory...
>>> * This is a software package, checking vignette directories...
>>> # of chunks: 40, # of eval=FALSE: 0 (0%)
>>> * Checking version number...
>>> * Checking version number validity...
>>> * Checking R Version dependency...
>>> * Checking biocViews...
>>> * Checking that biocViews are present...
>>> * Checking for non-trivial biocViews...
>>> * Checking that biocViews come from the same category...
>>> * Checking biocViews validity...
>>> * Checking for recommended biocViews...
>>> * Checking build system compatibility...
>>> * Checking for blank lines in DESCRIPTION...
>>> * Checking for whitespace in DESCRIPTION field names...
>>> * Checking that Package field matches dir/tarball name...
>>> * Checking for Version field...
>>> * Checking for valid maintainer...
>>> * Checking unit tests...
>>> * NOTE: Consider adding unit tests. We strongly encourage them. See
>>>
>>>http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>A
>>>na
>>> lysisStatistics.Rd:106: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>e
>>>xp
>>> ortBS.Rd:77: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>I
>>>nt
>>> erPETs-class.Rd:23: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>I
>>>nt
>>> raPETs-class.Rd:23: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>M
>>>AC
>>> PET.Rd:53: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ea
>>> kCallerUlt.Rd:186: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ea
>>> kCallerUlt.Rd:188: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ea
>>> kFinder.Rd:97: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ea
>>> ksToGRanges.Rd:68: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ET
>>> Classification.Rd:138: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>P
>>>ET
>>> sToGRanges.Rd:73: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>p
>>>lo
>>> t.Rd:168: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>R
>>>eg
>>> ionSegmentation.Rd:80: unknown macro '\insertRef'
>>> Warning in parse_Rd(infile) :
>>>
>>>
>>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw4gn/T//RtmpNOtV3V/MACPET/man/
>>>S
>>>am
>>> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef'
>>> W
Re: [Bioc-devel] Question about sumbition process and biocviews
On 11/08/2016 08:26 AM, Ioannis Vardaxis wrote:
Create a folder \inst and place the REFERENCES.bib in it. (see attached)
Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}.
You have to have the Rdpack installed.
when I do that (see
https://github.com/mtmorgan/PkgA/tree/parse-Rd-insertRef) and run R CMD
build I see
$ R CMD build PkgA
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
Warning: /tmp/RtmpFDYMzj/Rbuild2deb22881ea6/PkgA/man/fun.Rd:13: unknown
macro '\insertRef'
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'
so the problem reported by BiocCheck is already visible in R CMD build.
Consulting the vignette for Rdpack
https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_references.pdf
I see that the solution is to add the line
RdMacros: Rdpack
to the DESCRIPTION file. I disagree with the package author that the
Rdpack package does not need to be in the Suggests: field; if it were
not there then how would something like the Bioconductor build system
know that it needed to have the Rdpack available when the package is built?
I updated the github repo with correct package.
Martin
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