[Bioc-devel] GenomicRanges 1.7.40

sort(gr)
Error in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE =
"IRanges") :
?'a', 'b', 'c' and 'd' must be integer vectors

I can't seem to be able to update to the latest GenomicRanges version
1.7.40:
Warning: dependency ?GenomicRanges (>= 1.7.40)? is not available
This leads to the ShortRead package failing to build:
Error : package ?GenomicRanges? 1.7.38 was found, but>= 1.7.40 is
required by ?ShortRead?


I also see all red flags for my Gviz package although I did not submit any
changes, and the culprit is in GenomicRanges in the 'sort' method:
example(GRanges)

sort(gr)
Error in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE =
"IRanges") :
   'a', 'b', 'c' and 'd' must be integer vectors


This is with my currently installed version 1.7.38. As mentioned above I
can't get the latest version through biocLite, and in order to build from
the svn I need to install some fairly large dependencies which takes
forever in the slow network I am in right now. So I am not sure whether
this issue was already fixed. Would be odd if the package would build
without such a bug causing an error?

Any idea what's happening?

Florian

sessionInfo()

R Under development (unstable) (2012-02-29 r58532)
Platform: i386-apple-darwin10.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomicRanges_1.7.38 IRanges_1.13.33      BiocGenerics_0.1.14
[4] BiocInstaller_1.3.9

loaded via a namespace (and not attached):
[1] stats4_2.15.0 tools_2.15.0



Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com

On 03/26/2012 10:07 AM, Hahne, Florian wrote:

I can't seem to be able to update to the latest GenomicRanges version
1.7.40:
Warning: dependency ?GenomicRanges (>= 1.7.40)? is not available
This leads to the ShortRead package failing to build:
Error : package ?GenomicRanges? 1.7.38 was found, but>= 1.7.40 is
required by ?ShortRead?


I also see all red flags for my Gviz package although I did not submit
any
changes, and the culprit is in GenomicRanges in the 'sort' method:
example(GRanges)

sort(gr)
Error in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE =
"IRanges") :
'a', 'b', 'c' and 'd' must be integer vectors


This is with my currently installed version 1.7.38. As mentioned above I
can't get the latest version through biocLite, and in order to build from
the svn I need to install some fairly large dependencies which takes
forever in the slow network I am in right now. So I am not sure whether
this issue was already fixed. Would be odd if the package would build
without such a bug causing an error?

Any idea what's happening?

GenomicRanges isn't passing R CMD build, so isn't available via
biocLite. You could

svn co
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges

and install with R CMD INSTALL

I don't really have insight on sort(gr).

Martin

Florian

sessionInfo()

R Under development (unstable) (2012-02-29 r58532)
Platform: i386-apple-darwin10.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomicRanges_1.7.38 IRanges_1.13.33 BiocGenerics_0.1.14
[4] BiocInstaller_1.3.9

loaded via a namespace (and not attached):
[1] stats4_2.15.0 tools_2.15.0



Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com