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Gary
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@gary-7967
Last seen 5.9 years ago
Hi,
Using qvalue as an exmple (the detail bleow), I cannot install it for R 3.5.0. It is the same for other packages I need. Anyone can help me? Many thanks.
> require(NBPSeq)
Loading required package: NBPSeq
Error: package or namespace load failed for ‘NBPSeq’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘qvalue’
> install.packages("qvalue")
Warning in install.packages :
package ‘qvalue’ is not available (for R version 3.5.0)
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
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] edgeR_3.22.2 limma_3.36.1 Rsubread_1.30.3
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 Rcpp_0.12.17 grid_3.5.0 locfit_1.5-9.1
[6] lattice_0.20-35
It is working. Thanks a lot. May I know the difference between biocLite() and install.packages()? Thanks a gain.
"biocLite()is the recommended way to install Bioconductor packages. There are several reasons for preferring this to the ‘standard’ way in which R pacakges are installed viainstall.packages().Bioconductor has a repository and release schedule that differs from R (Bioconductor has a ‘devel’ branch to which new packages and updates are introduced, and a stable ‘release’ branch emitted once every 6 months to which bug fixes but not new features are introduced).
A consequence of the mismatch between R and Bioconductor release schedules is that the Bioconductor version identified by
install.packages()is sometimes not the most recent ‘release’ available. For instance, an R minor version may be introduced some months before the next Bioc release. After the Bioc release the users of the R minor version will be pointed to an out-of-date version of Bioconductor."From: https://www.bioconductor.org/install/#why-biocLite