Hello,
I'm experiencing an issue when trying to install the "aaMap" package with its dependencies. This is exactly what I did, first the Biobase import, then aaMap but I keep getting the Warning message? I've pasted my sequence below:
> biocLite("Biobase")
BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘Biobase’ trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/Biobase_2.40.0.tgz' Content type 'application/x-gzip' length 2350360 bytes (2.2 MB) ================================================== downloaded 2.2 MB
So then I try installing the "aaMap" package with its dependencies:
> biocLite("aaMap") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘aaMap’ Warning message: package ‘aaMap’ is not available (for R version 3.5.1)
That didn't work, so I go back and load the Biobase library:
> library(Biobase) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
One more try at loading aaMap:
> biocLite("aaMap") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘aaMap’ Warning message: package ‘aaMap’ is not available (for R version 3.5.1)
Again, warning message; however, I have no trouble installing the "ALL" dataset - see below, everything installed just fine!?!
> biocLite("ALL") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘ALL’ installing the source package ‘ALL’ trying URL 'https://bioconductor.org/packages/3.7/data/experiment/src/contrib/ALL_1.22.0.tar.gz' Content type 'application/x-gzip' length 11401913 bytes (10.9 MB) ================================================== downloaded 10.9 MB * installing *source* package ‘ALL’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ALL) The downloaded source packages are in ‘/private/var/folders/hv/9fdmt1rj7zd6_6kqywsmplm40000gn/T/RtmpJkiUA9/downloaded_packages’
What am I doing wrong?
In case it matters, below is the version I'm running on my mac:
R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit)
Thank you - for some reason I started to think the aaMap as a package similar to the ALL pkg.