aaMap Import "Not Available"
1
0
Entering edit mode
@detroitdrive-16757
Last seen 5.4 years ago

 

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)

 

 

bioconductor biobase aaMap • 1.4k views
ADD COMMENT
2
Entering edit mode
rreck ▴ 20
@rreck-12488
Last seen 6.3 years ago
Fairfax County, VA

I can't be sure but based on my research it looks as though there isnt a package called aaMap at all. Rather there is a data set that is loaded

 data(aaMap)

see:

https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/data%3AaaMap

ADD COMMENT
0
Entering edit mode

Thank you - for some reason I started to think the aaMap as a package similar to the ALL pkg.  

ADD REPLY

Login before adding your answer.

Traffic: 634 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6