[Bioc-devel] No vignette

[Kristoffer Vitting-Seerup]

Hi

I finally have the devel version of my R package IsoformSwitchAnalyzeR
working (sorry I did not make it before the 1.17 release, but a new
dependency was only approved last second).

But now the devel version

does not seem to have a vignette. Does anybody have an idea why that is?
The vignette seems to be build and work during the automated checks.


Once that is fixed I'll push the devel changes into the main branch to have
IsoformSwitchAnalyzeR working again.

-- 
Cheers
Kristoffer

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[Bioc-devel] How to handle namespace/import of Rcurl

[Kristoffer Vitting-Seerup]

Hi Devel

I've recently added a function which relies on Rcurl but I'm having trouble
figuring out how to handle it in the namespace/import since it behaves
differently from other packages I rely on.

As seen here
I
currently I get a warning stating:
"*'::' or ':::' import not declared from: 'RCurl'*"

Due to inclusion of this code on one of my functions:

*RCurl::url.exists(isoformExonAnnoation)*

I've over the last couple of weeks tried several different things to avoid
warnings:
- Added it to namespace (*importFrom("RCurl", "*url.exists*" *)
- Imported the entire package in the namespace
- Added it to the Imports in the DESCRIPTION

For all of these I keep getting errors or warnings saying this is not
necessary for RCurl. Can somebody help me out with what the proper way to
avoid the warning above without causing any other errors/warning?

Cheers
Kristoffer

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[Bioc-devel] NEWS not updated on devel site

[Kristoffer Vitting-Seerup]

I just noticed that on the devel site for my package

the NEWS file linked to in the "Documentation" tab (linking to this
)
is outdated. The current version of the package in devel is 1.5.3 but the
NEWS tab refers to an older version (1.5.1). I checked by downloading the
source files and the NEWS file there contain info about 1.5.3. Are the NEWS
files parsed slower?

Kindest Regard
Kristoffer

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[Bioc-devel] How to solve warnings generated by loading other packages

[Kristoffer Vitting-Seerup]

Hi Everybody

I'm currently in the process of adding my newest R package to Bioconductor
and the last issue I need to solve i a warning generated when loading other
packages (which I depend on) due to functions with identical names in those
packages.

More specifcally I get this error:

* checking whether package 'IsoformSwitchAnalyzeR' can be installed
... [33s] WARNING
Found the following significant warnings:
  Warning: replacing previous import 'plyr::desc' by 'IRanges::desc'
when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'GenomicRanges::promoters' by
'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'plyr::count' by
'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'

Which registre with a warning (only) on tokay2 (windows).

How do I solve this problem?

In advance - thanks.

The details about the submission and package can be found here:
https://github.com/Bioconductor/Contributions/issues/349
http://bioconductor.org/spb_reports/IsoformSwitchAnalyzeR_buildreport_20170421060205.html
https://github.com/kvittingseerup/IsoformSwitchAnalyzeR

-- 
Kindest regards
Kristoffer Vitting-Seerup, PhD
Postdoctoral Researcher
Sandelin Lab

Bioinformatics Centre | Biotech Research & Innovation Centre (BRIC)
Dep. Of Biology
University of Copenhagen
Building 1, 3rd floor, office 3 (1-3-03)
Ole Maaløes Vej 5
DK-2200 Copenhagen N
Denmark
http://binf.ku.dk | http://www.bric.ku.dk
Skype id: k.vitting.seerup

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[Bioc-devel] GIntervalTree objects are corrupted during save/load

[Kristoffer Vitting-Seerup]

Hi bioc-devel

I’ve fond an error in the usage of GIntervalTree:

 test - GRanges(seqnames='Chr1', range=IRanges(start=10,end=20))
 test
GRanges with 1 range and 0 metadata columns:
  seqnamesranges strand
 Rle IRanges  Rle
  [1] Chr1  [10, 20]  *

this object I can save and load without problem:

save(test, file='test.Rdata')
 rm(test)
 load('test.Rdata')
 test
GRanges with 1 range and 0 metadata columns:
  seqnamesranges strand
 Rle IRanges  Rle
  [1] Chr1  [10, 20]  *


But if I convert to to a GIntervalTree (for faster overlap finding) I get a 
fatal error when loading:

test2 - GIntervalTree(test)
 test2
GIntervalTree with 1 range and 0 metadata columns:
  seqnamesranges strand
 Rle IRanges  Rle
  [1] Chr1  [10, 20]  *
 save(test2, file='test2.Rdata')
 rm(test2)
 load('test2.Rdata')
 test2
GIntervalTree with 1 range and 0 metadata columns:

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

Traceback:
 1: .Call(.NAME, ..., PACKAGE = PACKAGE)
 2: .Call2(fun, object@ptr, ..., PACKAGE = IRanges)
 3: .IntervalForestCall(from, asIRanges)
 4: asMethod(object)
 5: as(x@ranges, IRanges)
 6: .GT_reorderValue(x, as(x@ranges, IRanges))
 7: .local(x, ...)
 8: ranges(x)
 9: ranges(x)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace


My session info:
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

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

other attached packages:
 [1] spliceR_1.5.0 plyr_1.8.1RColorBrewer_1.0-5
VennDiagram_1.6.5 cummeRbund_2.7.1  Gviz_1.9.4
rtracklayer_1.25.8GenomicRanges_1.17.14 GenomeInfoDb_1.1.5
IRanges_1.99.13  
[11] S4Vectors_0.0.6   fastcluster_1.1.13reshape2_1.4  
ggplot2_0.9.3.1   RSQLite_0.11.4DBI_0.2-7 
BiocGenerics_0.11.2  

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.27.6 BBmisc_1.6   BSgenome_1.33.5  
BatchJobs_1.2Biobase_2.25.0   BiocParallel_0.7.0   
Biostrings_2.33.8Formula_1.1-1GenomicAlignments_1.1.10
[10] GenomicFeatures_1.17.6   Hmisc_3.14-4 MASS_7.3-33  
R.methodsS3_1.6.1RCurl_1.95-4.1   Rcpp_0.11.1  
Rsamtools_1.17.14VariantAnnotation_1.11.5 XML_3.98-1.1   
[19] XVector_0.5.6biomaRt_2.21.0   biovizBase_1.13.7
bitops_1.0-6 brew_1.0-6   cluster_1.15.2   
codetools_0.2-8  colorspace_1.2-4 dichromat_2.0-0 
[28] digest_0.6.4 fail_1.2 foreach_1.4.2
gtable_0.1.2 iterators_1.0.7  lattice_0.20-29  
latticeExtra_0.6-26  matrixStats_0.8.14   munsell_0.4.2   
[37] proto_0.3-10 scales_0.2.4 sendmailR_1.1-2  
splines_3.1.0stats4_3.1.0 stringr_0.6.2
survival_2.37-7  tools_3.1.0  zlibbioc_1.11.1  



-- 
Kindest regards
Kristoffer Vitting-Seerup, cand.scient. (M.Sc.), 
Ph.D Fellow
Sandelin Group

Bioinformatics Centre | Biotech Research  Innovation Centre (BRIC), Dep. Of 
Biology
University of Copenhagen
Building 1, 3th floor, office 3 (1-3-03)
Ole Maaløes Vej 5
DK-2200 Copenhagen N
Denmark
http://binf.ku.dk | http://www.bric.ku.dk







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