Question: (Closed) Bioconductor Dataset "aaMAP" Import "Not Available"
0
gravatar for oars
8 months ago by
oars150
oars150 wrote:

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)
aamap biobase bioconductor R • 317 views
ADD COMMENTlink written 8 months ago by oars150
1

Hello oars!

We believe that this post can be best addressed elsewhere.

Please search/ask https://support.bioconductor.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 8 months ago • written 8 months ago by RamRS21k
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