[Bioc-devel] package not available (for R version 3.2.3)

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Tue Aug 9 15:49:17 CEST 2016

Hi Etienne,

The BiocInstaller package, which contains the biocLite() function, looks
in different Bioconductor repositories depending on what version of R is
being run. BiocInstaller 1.20.* (your code below) was looking in the
previous release repository (Bioconductor 3.1 and R 3.2) where the
biosigner package did not exist. The first version of BiocInstaller that
will 'find' your package is 1.22.* which is associated with the current
R 3.3 release.

biosigner is a new package in release which means it was developed
against R 3.3. While the package may work with earlier versions of R or
other dependencies there are no guarantees. Versions do matter.
BiocInstaller attempts to both minimize installation problems and
provide reproducible results by drawing from a repository tied to
particular version of R and Bioconductor.


On 08/09/2016 06:03 AM, THEVENOT Etienne 207099 wrote:
> Dear Bioc team,
> A friend of mine had the following trouble to install the biosigner package on R 3.2.3.
> I do not understand why the package would require a dedicated version of R (in particular >3.2.3) except that it uses S4 methods, and if/how I have to specify an R version within the package (note that the ropls package, which biosigner depends upon, seemed to require also a recent version of R).
> I thank you very much in advance for your answer.
> Kind Regards,
> Etienne.
>> source("https://bioconductor.org/biocLite.R")
> Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
> A new version of Bioconductor is available after installing the most recent
>   version of R; see http://bioconductor.org/install
>> biocLite("biosigner")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
> Installing package(s) 'biosigner'
> Old packages: 'AnnotationDbi', 'ape', 'BH', 'boot', 'car', 'caret', 'cluster',
>   'CORElearn', 'curl', 'DBI', 'devtools', 'digest', 'dplyr', 'evaluate',
>   'FactoMineR', 'formatR', 'ggplot2', 'git2r', 'gridExtra', 'gtable', 'highr',
>   'Hmisc', 'htmltools', 'httr', 'IRanges', 'jsonlite', 'knitr', 'latticeExtra',
>   'lazyeval', 'lme4', 'maps', 'Matrix', 'memoise', 'mgcv', 'mime', 'mnormt',
>   'msm', 'mtbls2', 'mzR', 'nlme', 'nnet', 'phangorn', 'phytools', 'plotrix',
>   'plyr', 'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rmarkdown',
>   'roxygen2', 'rstudioapi', 'rversions', 'S4Vectors', 'scales',
>   'scatterplot3d', 'stringi', 'survival', 'XML', 'xml2', 'xtable'
> Update all/some/none? [a/s/n]: n
> Warning message:
> package 'biosigner' is not available (for R version 3.2.3)
> When I updated my R version to the latest it worked. I'll check which version is used in biosigner. But unless there is a good reason to have to use R > 3.2.3, I would allow the package to install on older versions (people don't update R on their desktops so often). I think you need to set that up on the config files of the package that you upload to bioconductor.
> Etienne Th�venot<http://etiennethevenot.pagesperso-orange.fr/index.html>
> Computational metabolomics
> CEA<http://www.cea.fr/english-portal>, LIST<http://www-list.cea.fr/index.php/en/>, Laboratory for data analysis and systems' intelligence<http://www-list.cea.fr/index.php/en/technological-research/research-programmes/ambient-intelligence/data-analysis>, MetaboHUB<http://www.metabohub.fr/index.php?lang=en>
> B�t. 565 (Digiteo Saclay<http://www-list.cea.fr/images/stories/decouvrir-le-cea-list/implantations/Coming_to_Digiteo_Saclay.pdf>), PC 192
> F-91191 Gif-sur-Yvette Cedex, France
> Tel: +33 (0)1 69 08 79 23
> E-mail: etienne.thevenot at cea.fr<mailto:etienne.thevenot at cea.fr>
> Workflow4metabolomics.org<http://workflow4metabolomics.org/>
> R�seau Francophone de M�tabolomique et Fluxomique<http://www.rfmf.fr/>
> 	[[alternative HTML version deleted]]

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