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Old 01-23-2010, 01:13 PM   #1
Wei-HD
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Default Shortread Package INSTALL

Hi All,

Sorry to ask a very basic question:

I downloaded ShortRead package from: http://www.bioconductor.org/packages...ShortRead.html

But can someone tell me how to load the ShortRead package, I could not install this package in R. Error always like this:

>library("ShortRead")
Error in library("ShortRead") : there is no package called 'ShortRead'

Did I choose the wrong directory?

Thanks in advance!
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Old 01-24-2010, 08:50 AM   #2
Bukowski
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Well you downloaded it, but you clearly haven't installed it.

source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")

using biocLite to install packages is much better than downloading the packages from the download page.

This information is on the package page (http://www.bioconductor.org/packages...ShortRead.html)

If you followed this procedure yet:

library(ShortRead)

doesn't work, we'll probably need some more information, such as what platform you're trying to install it on.
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Old 01-24-2010, 11:19 PM   #3
Wei-HD
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Thanks Bukowski!

I installed shortread. But when I open R each time and type in "library(ShortRead)", it always repeat this step.

Loading required package: IRanges

Attaching package: 'IRanges'


The following object(s) are masked from package:base :

cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: lattice
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Old 01-25-2010, 01:18 AM   #4
byb121
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I get the same message as well. But everything works fine for me.

This will explain what "mask" means:
http://tolstoy.newcastle.edu.au/R/e2...6/10/3476.html
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Old 01-25-2010, 03:29 AM   #5
maubp
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Quote:
Originally Posted by Wei-HD View Post
Thanks Bukowski!

I installed shortread. But when I open R each time and type in "library(ShortRead)", it always repeat this step.

Loading required package: IRanges

Attaching package: 'IRanges'


The following object(s) are masked from package:base :

cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: lattice
That's normal - its just R telling you about what it has just loaded.
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Old 09-14-2010, 10:42 AM   #6
danela
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I-ve tried to install it, but it installs the 1.4 version and I need 1.6.2, does it have to do with the fact that I have installed the 1.4 and am trying to re-install it?

How can I upgrade?
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Old 09-15-2010, 06:45 AM   #7
Simon Anders
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You need to upgrade R to the current version.
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Old 04-29-2014, 05:18 AM   #8
archi
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Hi All,
I have tried installing the ShortRead package many times now using
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
but everytime I get an error message when I use library(ShortRead).
My R version is R 3.0.2

While the installation process is going on I get messages like
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name...
rm: cannot remove `a.out.dSYM': Is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/XML’
ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’

The downloaded packages are in
‘/tmp/RtmpTluoUe/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘Rsamtools’ had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘ShortRead’ had non-zero exit status
6: 'cluster' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
'KernSmooth' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
'mgcv' cannot be updated, installed directory '/usr/lib/R/library'
not writeable
'nnet' cannot be updated, installed directory '/usr/lib/R/library'
not writeable
'survival' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
>

Kindly suggest something asap.
thanks in advance.
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Old 04-29-2014, 05:47 AM   #9
maubp
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You are trying to install the library at system level in /usr/lib/R/library so try doing this with sudo (assuming you have admin rights).
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Old 04-29-2014, 06:26 AM   #10
archi
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can u please elaborate??
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Old 04-29-2014, 06:26 AM   #11
Simon Anders
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No, that's not the issue.

This here is the error you should have paid attention to:

Quote:
Cannot find xml2-config
It means that you have not installed the header files for the XML2 systems library. Do so using your package manager. For example, in Ubuntu, use the Software Centre to install the package "libxml2-dev".
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Old 04-29-2014, 06:30 AM   #12
archi
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Also, can u please tell me how to install libcurl on ubuntu for R 3.0.2
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Old 04-29-2014, 06:39 AM   #13
maubp
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Quote:
Originally Posted by archi View Post
Also, can u please tell me how to install libcurl on ubuntu for R 3.0.2
Try:
Code:
sudo apt-get install libxml2-dev
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Old 04-29-2014, 06:40 AM   #14
maubp
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Quote:
Originally Posted by Simon Anders View Post
No, that's not the issue.

This here is the error you should have paid attention to...
Yeah, that was the immediate problem - I missed that.
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Old 04-29-2014, 06:47 AM   #15
archi
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I have installed libxml2-dev but now I'm getting these error.
Sorry for asking such basic doubts but please do help
Thanks a lot.

installing to /home/linux/R/x86_64-pc-linux-gnu-library/2.14/XML/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) :
the supplied generic function definition for ‘xmlClone’ does not seem to call 'standardGeneric'; no methods will be dispatched!
in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (XML)
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
* removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’

The downloaded packages are in
‘/tmp/RtmpTluoUe/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘Rsamtools’ had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘ShortRead’ had non-zero exit status
5: 'cluster' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
'KernSmooth' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
'mgcv' cannot be updated, installed directory '/usr/lib/R/library'
not writeable
'nnet' cannot be updated, installed directory '/usr/lib/R/library'
not writeable
'survival' cannot be updated, installed directory
'/usr/lib/R/library' not writeable
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Old 04-29-2014, 06:55 AM   #16
archi
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I think I need libcurl (version 7.14.0 or higher) as I'm working on linux but can't figure out how to do that. Can someone please suggest something asap.
thanks in advance
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Old 04-29-2014, 07:00 AM   #17
archi
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Thanks a lot everyone. I have successfully installed ShortRead package on my system.
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Old 04-29-2014, 07:09 AM   #18
maubp
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Can you explain how you solved the remaining problems? That would help anyone else reading this thread in future (e.g. from a Google search with the error message).
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Old 04-29-2014, 09:57 PM   #19
archi
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Yes,sure.
after installing libxml,the main problem was having libcurl on my system.As I'm working on linux,libcurl has to be explicitly installed and I did that using Ubuntu software center.After that type source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
and it gets installed.
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Old 04-29-2014, 11:19 PM   #20
Simon Anders
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You should add that you have not only installed the curl library but also the header files, which are required to compile other stuff (such as Bioconductor packages) using the library. Therefore, it is important to chose the 'dev 'package ('libcurl-dev', not only 'libcurl' and 'libxml2-dev', not only 'libxml2') when installing system libraries that an R package needs.
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