Question: Installing Bioclite.R Package
0
gravatar for louiseapps2
3.6 years ago by
United Kingdom
louiseapps20 wrote:

Hiya,

I'm currently taking a systems biology course and I need to use bioconductor for genome analysis but I'm having an issue installing bioclite.  I'm using the address that I was given which is "http://bioconductor.org/bioclite.R" to install the package but I am just getting a Bioconductor page saying "The page you were looking for was not found." (I have also tried https but the same thing happens).

Please help! Where can I get this package from?

Louise

install bioclite • 15k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by louiseapps20
Answer: Installing Bioclite.R Package
1
gravatar for Aaron Lun
3.6 years ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Well, you need to capitalize the "L" in biocLite, for starters. This should be a valid link: http://bioconductor.org/biocLite.R. Perhaps you should also have a look at the installation instructions here.

ADD COMMENTlink modified 3.6 years ago by Martin Morgan ♦♦ 23k • written 3.6 years ago by Aaron Lun24k
I tried that already and all I get is a shitton of code, which I've read through. no options to download and absolutely zero sense made.  I've read and re-read the instruction stuff and it makes no sense to me either. (your link to the instructions doesn't work btw).
ADD REPLYlink written 3.6 years ago by louiseapps20
1

I'm not really familiar with the 'shitton' unit of measurement; sounds sort of french? The installation instructions tell you that you must first install and start the latest version of R, and then enter the command

source("http://bioconducor.org/biocLite.R")

Have you followed the link to install the latest version of R? After starting R, have you entered the command above? If you get that far, then the posting guide 'key points' suggests that you include your attempt and the output of sessionInfo(). This does require that some code be inserted into your question, but I think the amount is less than a shitton and at any rate the internet can handle that. Here's what I see:

> source("http://bioconductor.org/biocLite.R")
Installing package into '/tmp'
(as 'lib' is unspecified)
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/BiocInstaller_1.20.1.tar.gz'
Content type 'application/x-gzip' length 15695 bytes (15 KB)
==================================================
downloaded 15 KB

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
    '/tmp/RtmpcRTZW8/downloaded_packages'
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> sessionInfo()
R version 3.2.2 Patched (2015-10-30 r69588)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.2

Your next step will be to choose the packages you wish to install; you would not wish to install all of Bioconductor. The 'biocViews' index is a good starting point, typically leading to a 'landing page' where there are specific installation instructions, e.g., for the 'Biobase' package

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("Biobase")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 Patched (2015-10-30
  r69588).
Installing package(s) 'Biobase'
also installing the dependency 'BiocGenerics'

trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz'
Content type 'application/x-gzip' length 38289 bytes (37 KB)
==================================================
downloaded 37 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/Biobase_2.30.0.tar.gz'
Content type 'application/x-gzip' length 1671178 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'append' in package 'BiocGenerics'
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'as.vector' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'do.call' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'grep' in package 'BiocGenerics'
Creating a new generic function for 'grepl' in package 'BiocGenerics'
Creating a new generic function for 'is.unsorted' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'lengths' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unlist' in package 'BiocGenerics'
Creating a new generic function for 'unsplit' in package 'BiocGenerics'
Creating a new generic function for 'IQR' in package 'BiocGenerics'
Creating a new generic function for 'mad' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
* DONE (BiocGenerics)
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
* installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c envir.c -o envir.o
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/home/mtmorgan/bin/R-3-2-branch/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/mtmorgan/bin/R-3-2-branch/lib -lR
installing to /tmp/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
* DONE (Biobase)

The downloaded source packages are in
    '/tmp/RtmpbqiZo0/downloaded_packages'

Your output might be different, depending on the platform you are using. You would then be in a position to actually use the software, starting with library(Biobase)

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Martin Morgan ♦♦ 23k

Yes I have the latest version of R. It's downloaded something but I've got different output to what you have. Guess I'll have to play around with it to see if it's done it right!  Thanks for your help.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by louiseapps20
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