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List:       bioc-devel
Subject:    Re: [Bioc-devel] BiocLite - our package is not available
From:       <j.d.ronde () nki ! nl>
Date:       2009-06-02 14:24:46
Message-ID: ECFF52D642618743AB4607E205B14F22141679CA () mstr-2 ! nki ! nl
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Hi Vincent and Sean,

Thank you for your replies. I'm sorry I did not include sessionInfo() before, I \
assumed that since other packages were downloading fine (like 'lumi' or 'limma') \
nothing was wrong on the client side. However, upon closer inspection I now see that \
biocLite is actually using the 2.2 branch in which our package was not yet available. \
I will update my R and most likely things will work out fine. Sorry for being dopey \
;)

Jorma
Ps For completeness, here's the sessionInfo:

> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32

locale:
LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MONETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252


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

From: Vincent Carey [mailto:stvjc@channing.harvard.edu]
Sent: dinsdag 2 juni 2009 16:12
To: Jorma de Ronde
Cc: bioc-devel@stat.math.ethz.ch
Subject: Re: [Bioc-devel] BiocLite - our package is not available

as you did not attach a sessionInfo() result it is hard to diagnose.  i just tried
biocLite("KCsmart", type="source") from R 2.10.0 and it downloaded and installed.  i \
also checked the 2.4/2.5 build logs and your package is building ok.  try again, and \
if it fails, send details on your R installation.
On Tue, Jun 2, 2009 at 9:46 AM, <j.d.ronde@nki.nl<mailto:j.d.ronde@nki.nl>> wrote:
Hi all,

Today I tried to download a package we created ('KCsmart', \
http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html) through biocLite:

source("http://bioconductor.org/biocLite.R")
biocLite("KCsmart")

I was a bit surprised to get the error
'Warning message:
package 'KCsmart' is not available

Through some further searching I tried to locate the package using
biocContribUrl <- sapply(Biobase::biocReposList(), contrib.url)
biocPkgs <- available.packages(biocContribUrl)
'KCsmart' %in% biocPkgs[, "Package"]

And this also results in a 'FALSE' reply. The package builds and checks without any \
errors and other packages download fine so I'm guessing there's nothing wrong on the \
client side. Is there something I can do to make the package available through \
biocLite?

Thanks in advance,
Jorma de Ronde

Jorma de Ronde, MSc
Molecular Biology (P2)
The Netherlands Cancer Institute
Plesmanlaan 121, 1066 CX Amsterdam
The Netherlands
Phone: +31 20 512 6909
Email: j.d.ronde@nki.nl<mailto:j.d.ronde@nki.nl><mailto:j.d.ronde@nki.nl<mailto:j.d.ronde@nki.nl>>
 http://bioinformatics.nki.nl/


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Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265

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