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Question: Package is not available for R version 3.5.0
0
gravatar for Gary
4 months ago by
Gary0
Gary0 wrote:

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
ADD COMMENTlink modified 4 months ago by Gordon Smyth35k • written 4 months ago by Gary0
1
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

qvalue is now on Bioconductor rather than CRAN so you need

biocLite("qvalue")

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth35k

It is working. Thanks a lot. May I know the difference between biocLite() and install.packages()? Thanks a gain.

ADD REPLYlink modified 4 months ago • written 4 months ago by Gary0
1

"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 via install.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

ADD REPLYlink written 4 months ago by mario.zanfardino150
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