[Bioc-devel] Chromosome order in GRangesForUCSCGenome

[Bernat Gel]

I'm downloading genome information from UCSC using the 
GRangesForUCSCGenome from rtracklayer and it seems that the chromosome 
order is incorrect (or at least non-canonical).


> seqlevels(GRangesForUCSCGenome(genome="hg19"))

[1] "chr1"  "chr2" "chr3"  "chr4" "chr5"
[6] "chr6"  "chr7" "chrX"  "chr8" "chr9"
[11] "chr10" "chr11" "chr12" "chr13" 
"chr14"
[16] "chr15" "chr16" "chr17" "chr18" 
"chr20"
[21] "chrY"  "chr19" "chr22" "chr21" 
"chr6_ssto_hap7"

[26] ...

With chrX before chr8  and Y before chr19.

And the same happens with SeqinfoForUCSCGenome(genome="hg19")

I know I could reorder them manually, but I'm downloading this from 
various genomes to cache them in a package (karyoploteR) and I'd rather 
not rely on manual sorting for that.


I'm quite sure it used to return them in the canonical order. Is there 
anything I'm missing or is it a bug somewhere?



Thanks a lot

Bernat




sessionInfo()
R Under development (unstable) (2016-11-07 r71637)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C 
LC_COLLATE=en_US.utf8 LC_MONETARY=en_US.utf8
 [6] LC_MESSAGES=en_US.utf8LC_PAPER=es_ES.UTF-8 
LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets  
methods   base


other attached packages:
 [1] testthat_1.0.2karyoploteR_0.99.8 biovizBase_1.23.2 
regioneR_1.7.1BSgenome_1.43.2 rtracklayer_1.35.1
 [7] Biostrings_2.43.2 XVector_0.15.0 GenomicRanges_1.27.18 
GenomeInfoDb_1.11.6   IRanges_2.9.14 S4Vectors_0.13.5

[13] BiocGenerics_0.21.1   memoise_1.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8   lattice_0.20-34 
Rsamtools_1.27.11 assertthat_0.1
 [5] digest_0.6.11 mime_0.5 
R6_2.2.0  plyr_1.8.4
 [9] backports_1.0.4   acepack_1.4.1 
RSQLite_1.1-2 httr_1.2.1
[13] ggplot2_2.2.1 BiocInstaller_1.25.3 
zlibbioc_1.21.0   GenomicFeatures_1.27.6
[17] lazyeval_0.2.0data.table_1.10.0 
rpart_4.1-10  Matrix_1.2-7.1
[21] checkmate_1.8.2   splines_3.4.0 
BiocParallel_1.9.4AnnotationHub_2.7.9
[25] stringr_1.1.0 foreign_0.8-67 
ProtGenerics_1.7.0RCurl_1.95-4.8
[29] biomaRt_2.31.3munsell_0.4.3 
shiny_0.14.2  httpuv_1.3.3
[33] base64enc_0.1-3   htmltools_0.3.5 
nnet_7.3-12   SummarizedExperiment_1.5.3
[37] tibble_1.2gridExtra_2.2.1 
htmlTable_1.8 interactiveDisplayBase_1.13.0
[41] Hmisc_4.0-2   XML_3.98-1.5 
crayon_1.3.2  GenomicAlignments_1.11.6
[45] bitops_1.0-6  grid_3.4.0 
xtable_1.8-2  gtable_0.2.0
[49] DBI_0.5-1 magrittr_1.5 
scales_0.4.1  stringi_1.1.2
[53] latticeExtra_0.6-28   Formula_1.2-1 
RColorBrewer_1.1-2ensembldb_1.99.10
[57] tools_3.4.0   dichromat_2.0-0 
Biobase_2.35.0survival_2.40-1
[61] yaml_2.1.14   AnnotationDbi_1.37.0 
colorspace_1.3-2  cluster_2.0.5

[65] VariantAnnotation_1.21.14 knitr_1.15.1


--

*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
b...@igtp.cat 
www.germanstrias.org 









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[Bioc-devel] question on package build

[????]

Hi

I have develop a Bioconductor package and submit the issue to build and check. 
It has passed the build and check on Windows and Mac OS. But I don't know why 
build takes less than 1 minute on Windows and Mac OS but more than 10 minutes 
on your  Linux machine? The report of build and check is on the below:
http://bioconductor.org/spb_reports/Trumpet_buildreport_20170313003039.html 

 
Teng Zhang
   
Thank you for your help
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Re: [Bioc-devel] question on package build

[Shepherd, Lori]

I can investigate this and see what was going on however, you deleted the first 
comment when submitting packages that included the link to your github 
repository.  Until you add the section agreeing to the Bioconductor terms of 
package review and include the link to your github repository we can not help 
you.  I made this comment on your issues page as well.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of  
<2573552...@qq.com>
Sent: Monday, March 13, 2017 8:46:19 AM
To: Bioc-devel
Subject: [Bioc-devel] question on package build

Hi

I have develop a Bioconductor package and submit the issue to build and check. 
It has passed the build and check on Windows and Mac OS. But I don't know why 
build takes less than 1 minute on Windows and Mac OS but more than 10 minutes 
on your  Linux machine? The report of build and check is on the below:
http://bioconductor.org/spb_reports/Trumpet_buildreport_20170313003039.html
Teng Zhang

Thank you for your help
[[alternative HTML version deleted]]

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Re: [Bioc-devel] Chromosome order in GRangesForUCSCGenome

[Michael Lawrence]

Looks like UCSC has started sorting the chromosomes by size.  I made 1.35.9
use sortSeqlevels() to normalize the order of them.

On Mon, Mar 13, 2017 at 3:05 AM, Bernat Gel  wrote:

> I'm downloading genome information from UCSC using the
> GRangesForUCSCGenome from rtracklayer and it seems that the chromosome
> order is incorrect (or at least non-canonical).
>
> > seqlevels(GRangesForUCSCGenome(genome="hg19"))
>
> [1] "chr1"  "chr2" "chr3"  "chr4" "chr5"
> [6] "chr6"  "chr7" "chrX"  "chr8" "chr9"
> [11] "chr10" "chr11" "chr12" "chr13"
> "chr14"
> [16] "chr15" "chr16" "chr17" "chr18"
> "chr20"
> [21] "chrY"  "chr19" "chr22" "chr21"
> "chr6_ssto_hap7"
> [26] ...
>
> With chrX before chr8  and Y before chr19.
>
> And the same happens with SeqinfoForUCSCGenome(genome="hg19")
>
> I know I could reorder them manually, but I'm downloading this from
> various genomes to cache them in a package (karyoploteR) and I'd rather not
> rely on manual sorting for that.
>
> I'm quite sure it used to return them in the canonical order. Is there
> anything I'm missing or is it a bug somewhere?
>
>
> Thanks a lot
>
> Bernat
>
>
>
>
> sessionInfo()
> R Under development (unstable) (2016-11-07 r71637)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 8 (jessie)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C
>  LC_COLLATE=en_US.utf8 LC_MONETARY=en_US.utf8
>  [6] LC_MESSAGES=en_US.utf8LC_PAPER=es_ES.UTF-8 LC_NAME=C
>LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4stats graphics  grDevices utils datasets
> methods   base
>
> other attached packages:
>  [1] testthat_1.0.2karyoploteR_0.99.8 biovizBase_1.23.2
>  regioneR_1.7.1BSgenome_1.43.2 rtracklayer_1.35.1
>  [7] Biostrings_2.43.2 XVector_0.15.0 GenomicRanges_1.27.18
> GenomeInfoDb_1.11.6   IRanges_2.9.14 S4Vectors_0.13.5
> [13] BiocGenerics_0.21.1   memoise_1.0.0
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.8   lattice_0.20-34 Rsamtools_1.27.11
>assertthat_0.1
>  [5] digest_0.6.11 mime_0.5 R6_2.2.0
> plyr_1.8.4
>  [9] backports_1.0.4   acepack_1.4.1 RSQLite_1.1-2
>  httr_1.2.1
> [13] ggplot2_2.2.1 BiocInstaller_1.25.3 zlibbioc_1.21.0
>GenomicFeatures_1.27.6
> [17] lazyeval_0.2.0data.table_1.10.0 rpart_4.1-10
> Matrix_1.2-7.1
> [21] checkmate_1.8.2   splines_3.4.0 BiocParallel_1.9.4
> AnnotationHub_2.7.9
> [25] stringr_1.1.0 foreign_0.8-67 ProtGenerics_1.7.0
>   RCurl_1.95-4.8
> [29] biomaRt_2.31.3munsell_0.4.3 shiny_0.14.2
> httpuv_1.3.3
> [33] base64enc_0.1-3   htmltools_0.3.5 nnet_7.3-12
>SummarizedExperiment_1.5.3
> [37] tibble_1.2gridExtra_2.2.1 htmlTable_1.8
>interactiveDisplayBase_1.13.0
> [41] Hmisc_4.0-2   XML_3.98-1.5 crayon_1.3.2
> GenomicAlignments_1.11.6
> [45] bitops_1.0-6  grid_3.4.0 xtable_1.8-2
>   gtable_0.2.0
> [49] DBI_0.5-1 magrittr_1.5 scales_0.4.1
> stringi_1.1.2
> [53] latticeExtra_0.6-28   Formula_1.2-1 RColorBrewer_1.1-2
> ensembldb_1.99.10
> [57] tools_3.4.0   dichromat_2.0-0 Biobase_2.35.0
>   survival_2.40-1
> [61] yaml_2.1.14   AnnotationDbi_1.37.0 colorspace_1.3-2
> cluster_2.0.5
> [65] VariantAnnotation_1.21.14 knitr_1.15.1
>
>
> --
>
> *Bernat Gel Moreno*
> Bioinformatician
>
> Hereditary Cancer Program
> Program of Predictive and Personalized Medicine of Cancer (PMPPC)
> Germans Trias i Pujol Research Institute (IGTP)
>
> Campus Can Ruti
> Carretera de Can Ruti, Camí de les Escoles s/n
> 08916 Badalona, Barcelona, Spain
>
> Tel: (+34) 93 554 3068
> Fax: (+34) 93 497 8654
> 08916 Badalona, Barcelona, Spain
> b...@igtp.cat 
> www.germanstrias.org 
>
> 
>
>
>
>
>
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] devel builds: oaxaca phase out

[Obenchain, Valerie]

oaxaca has been removed from the build report and toluca2 is now the
official Mac devel builder. Herve has applied all system updates to
toluca2 and is smoothing out the final kinks. Lori is finalizing the
transition of the Single Package Builder from oaxaca to toluca2 and once
that's done oaxaca will be shut down.

Thanks for your patience while we dealt with the failing oaxaca and
worked through setting up the new machine.

Valerie



This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function

[Jason.Ross]

Thanks Hervé and Henrik, I have also been experiencing the same issues. I 
innocently typed "sudo apt-get upgrade" in Ubuntu and this broke my 
Bioconductor install.

Regards,
Jason

-Original Message-
From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Henrik 
Bengtsson
Sent: Friday, 10 March 2017 5:09 PM
To: Hervé Pagès 
Cc: bioC-devel 
Subject: Re: [Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : 
could not find symbol "recursive" in environment of the generic function

Thanks Hervé.  I can confirm that reinstalling packages from R 3.3.2 to R 3.3.3 
solved the problem:

https://github.com/HenrikBengtsson/globals/commit/f9ff3a092d1712258aab2d01277665abec7dfa32

/Henrik

On Thu, Mar 9, 2017 at 5:52 PM, Hervé Pagès  wrote:
> Hi Henrik,
>
> See here for similar problems reported earlier on our support site:
>
>   https://support.bioconductor.org/p/93347/#93373
>   https://support.bioconductor.org/p/93590/#93595
>
> I think you need to reinstall your packages after updating to R 3.3.
>
> API compatibility across minor R releases is a myth :-/
>
> H.
>
>
> On 03/09/2017 05:38 PM, Henrik Bengtsson wrote:
>>
>> Hi. FYI / Is anyone else experiencing:
>>
>> Error in c(x, values) :
>>   could not find symbol "recursive" in environment of the generic 
>> function
>>
>> errors for some Bioconductor packages when running under R 3.3.3 
>> while they don't occur with R 3.3.2?  This seems realted to the 
>> following R
>> 3.3.3 NEWS entry:
>>
>> c()'s argument use.names is documented now, as belonging to the (C
>> internal) default method. In “parallel”, argument recursive is also 
>> moved from the generic to the default method, such that the formal 
>> argument list of base generic c() is just (...).
>>
>> One quick example is:
>>
>> $ R --vanilla
>>>
>>> example("callLOH", package = "PureCN")
>>
>> [...]
>>>
>>> head(callLOH(purecn.example.output))
>>
>> Error in c(x, values) :
>>   could not find symbol "recursive" in environment of the generic 
>> function
>>
>>> traceback()
>>
>> 24: c(x, values)
>> 23: append(mcols(gr), slot(x, "fixed"))
>> 22: append(mcols(gr), slot(x, "fixed"))
>> 21: .local(x, ...)
>> 20: rowRanges(x)
>> 19: rowRanges(x)
>> 18: (function (x, ...)
>> standardGeneric("start"))(x = rowRanges(x), ... = ...)
>> 17: do.call(start, list(x = rowRanges(x), ... = ...))
>> 16: do.call(start, list(x = rowRanges(x), ... = ...))
>> 15: start(res$input$vcf)
>> 14: start(res$input$vcf)
>> 13: split(start(res$input$vcf), 
>> as.character(seqnames(res$input$vcf)))
>> 12: vapply(split(start(res$input$vcf),
>> as.character(seqnames(res$input$vcf))),
>> function(x) c(min(x), max(x)), c(min = double(1), max =
>> double(1)))
>> 11: t(vapply(split(start(res$input$vcf),
>> as.character(seqnames(res$input$vcf))),
>> function(x) c(min(x), max(x)), c(min = double(1), max =
>> double(1
>> 10: withCallingHandlers(expr, warning = function(w)
>> invokeRestart("muffleWarning"))
>> 9: suppressWarnings(t(vapply(split(start(res$input$vcf),
>> as.character(seqnames(res$input$vcf))),
>>function(x) c(min(x), max(x)), c(min = double(1), max =
>> double(1)
>> 8: .getArmLocations(res)
>> 7: callLOH(purecn.example.output)
>> 6: head(callLOH(purecn.example.output)) at Rex657e3e41cba7#8
>> 5: eval(expr, envir, enclos)
>> 4: eval(ei, envir)
>> 3: withVisible(eval(ei, envir))
>> 2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
>>getOption("prompt")), continue.echo = paste0(prompt.prefix,
>>getOption("continue")), verbose = verbose, max.deparse.length 
>> = Inf,
>>encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
>> 1: example("callLOH", package = "PureCN")
>>
>>> sessionInfo()
>>
>> R version 3.3.3 (2017-03-06)
>> Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 
>> LTS
>>
>> 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] stats4parallel  stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] PureCN_1.2.3   VariantAnnotation_1.20.2
>>  [3] Rsamtools_1.26.1   Biostrings_2.42.1
>>  [5] XVector_0.14.0 SummarizedExperiment_1.4.0
>>  [7] Biobase_2.34.0 GenomicRanges_1.26.3
>>  [9] GenomeInfoDb_1.10.3IRanges_2.8.1
>> [11] S4Vectors_0.12.1   BiocGenerics_0.20.0
>> [13] DNAcopy_1.48.0
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.9  AnnotationDbi_1.36.2
>> GenomicAlignments_1.10.0
>>  [4] zlibbioc_1.20.0  BiocParallel_1.8.1   BSgenome_1.42.0
>>  [7] lattice_0.20-34  tools_3.3.3  grid_3.3.3
>> [10] data.table_1.

[Bioc-devel] GRangesList Conversion Fails For Unstranded Sequencing Data

[Dario Strbenac]

Good day,

countOverlaps doesn't work for a GAlignmentPairs object with strandMode set to 
0. This is because of an oversight in the grglist function. It has an if 
statement that checks whether the strand mode is 1 or 2. Then, it tries to 
subset the variable 'x_unlisted'. However, if strand mode is 0, neither of the 
conditional sections of code are executed and Error in .local(x, use.names, 
use.mcols, ...) : object 'x_unlisted' not found happens because the 
'x_unlisted' variable has not been created. It's a surprise no one else has 
encountered this bug before.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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