[Bioc-devel] package not available (for R version 3.2.3)
Dear Etienne, Bioconductor versions are linked to R versions. As the biosigner package is a recent addition to Bioconductor (Bioc version 3.3), it will require a recent R version, i.e. the R version that was current when Bioc 3.3 was released. That is how things are, guaranteeing a coherent set of functioning set of packages for a specific Bioc versions. As a result, if a users want to use recent packages (as in newly added to Bioc or new versions/features), they will have to install a recent R. Best wishes, Laurent
On 9 August 2016 14:02, 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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Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/