DBI and RSQLite Errors plus other Warnings when Installing CummeRbund

[jmwhitha]

Hello RNA Seq community,

Could someone please help me? I am using the command "source('http://www.bioconductor.org/biocLite.R')
biocLite('cummeRbund')" in the R environment, and my output is:

ERROR: dependency ‘DBI’ is not available for package ‘RSQLite’
* removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/RSQLite’
ERROR: dependency ‘RSQLite’ is not available for package ‘cummeRbund’
* removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/cummeRbund’

The downloaded packages are in
‘/tmp/Rtmp8pQWJT/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘RSQLite’ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status
3: 'cluster' cannot be updated, installed directory '/usr/lib/R/library' not
writeable
'foreign' 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
'rpart' cannot be updated, installed directory '/usr/lib/R/library' not
writeable
'survival' cannot be updated, installed directory '/usr/lib/R/library' not
writeable

[jmwhitha]

Hello RNA Seq community,

Sorry, I think I posted this at a time when no would answer it.

Could someone please help me? I am using the command "source('http://www.bioconductor.org/biocLite.R')
biocLite('cummeRbund')" in the R environment, and my output is:

ERROR: dependency ‘DBI’ is not available for package ‘RSQLite’
* removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/RSQLite’
ERROR: dependency ‘RSQLite’ is not available for package ‘cummeRbund’
* removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/cummeRbund’

The downloaded packages are in
‘/tmp/Rtmp8pQWJT/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘RSQLite’ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status
3: 'cluster' cannot be updated, installed directory '/usr/lib/R/library' not
writeable
'foreign' 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
'rpart' cannot be updated, installed directory '/usr/lib/R/library' not
writeable
'survival' cannot be updated, installed directory '/usr/lib/R/library' not
writeable

[GenoMax]

You need to install the following packages at a minimum:

http://cran.r-project.org/web/packages/DBI/index.html

http://cran.r-project.org/web/packages/RSQLite/index.html

Check the dependancy section for cummerbund package for anything else you may need: http://www.bioconductor.org/packages...ummeRbund.html

There also appears to be an issue where /usr/lib/R/library is not writable from the account you are trying to install the packages from.

I remember you being the "sys admin" for this system from past posts. Try doing the cummerbund install as a user with write privileges to that directory path.

[jmwhitha]

Good morning GenoMax,

Thank you for the quick reply!

Before posting this topic, I used the following commands to get DBI and RSQLite.
wget http://cran.fhcrc.org/src/contrib/DBI_0.2-7.tar.gz -O DBI_0.2-7.tar.gz
tar zxvf DBI_0.2-7.tar.gz
wget http://cran.r-project.org/src/contri..._0.11.3.tar.gz -O RSQLite_0.11.3.tar.gz
tar zxvf RSQLite_0.11.3.tar.gz

I guess that's not enough code to get the job done though. I also just noticed that DBI requires R version >= 2.15.0

The following command only gets me version 2.14.1 though.
sudo apt-get install r-base-core

What commands can I use to get >= 2.15.0?


Concerning the following, would I use the command?
sudo chmod 777 /usr/lib/R/library

Could you break the second sentence down for me a little more. I'm not really sure what installing as a user with write privileges to that directory path entails.

You need to install the following packages at a minimum:

There also appears to be an issue where /usr/lib/R/library is not writable from the account you are trying to install the packages from.

I remember you being the "sys admin" for this system from past posts. Try doing the cummerbund install as a user with write privileges to that directory path.

Thank you so much!
Jason

[GenoMax]

Jason,

Just downloading the packages in not enough to install them. Here is a reference for installing packages in R. It is possible to install R libraries under your own user directory (so you do not need to write in /usr area, which is system reserved).

Since you are the only user on your system it may be worth trying the install cummerBund by starting R as root. This should give you write permissions to the /usr/lib/R/library directory.

sudo R

Then in R do the "cummerBund" install.

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

If that works then remember to close R and then start R back as a regular user.

[jmwhitha]

Thanks for the document.

Most of the installation seems to work, except DBI still needs a newer version of R.

I tried to use the document to get 2.15.0 using the following code:

wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz
tar xf R-2.15.0.tar.gz
#Before executing ./configure you need to get X11 headers
#http://forum.linuxcareer.com/threads...-not-available
sudo apt-get install xorg-dev
./configure
make

Again, this seemed to work great, except when I execute "R", it's still using 2.14.1. How do I get it to launch the 2.15.0 version?

Thank you again!

[jmwhitha]

Oh, I figured that out.

I just went into ~/bin/R-2.15.0/bin and executed ./R

Installation of cummeRbund worked in this version!
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

Unfortunately, executing just "R" gives me the old version.

Can I do something to make it so that when I execute "R" without setting a path, it gives me the new version?

Thank you!

[GenoMax]

Oh, I figured that out.

I just went into ~/bin/R-2.15.0/bin and executed ./R

Installation of cummeRbund worked in this version!
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

Unfortunately, executing just "R" gives me the old version.

Can I do something to make it so that when I execute "R" without setting a path, it gives me the new version?

Thank you!

Open a new terminal window. Check to see where is the default "R" that you are getting is located.

which R

Then do a

ls -l full_path_to_location_from_above_command

Depending on what the answer is we can decide on an appropriate method.

[jmwhitha]

Thanks GenoMax,

Just was emailing with another friend and he helped me get these two commands...

sudo rm -f ./R #after cd'ing to the directory containing the old version /usr/bin
sudo ln -s /path/to/new/R R #where R is an executable, not a directory

...and they worked great!!

PROBLEM SOLVED

God bless,
Jason

[Baoqing]

still errors

Hey, guys

I was following your discussion, but still have error messages, could you share some thoughts on this, thanks a lot!
:

wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz

tar xf R-2.15.0.tar.gz

sudo apt-get install xorg-dev

./configure

make

~/bin/R-2.15.0/bin

./R

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

However, still have the following errors:
The downloaded source packages are in
‘/tmp/Rtmpk15EqK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status

[GenoMax]

It appears that you are missing some libraries:

If this is ubuntu then

sudo apt-get install libxml2-dev libxml2 curl curl-devel

You may also need to install some R-packages. Check the "depends" section from the cummerBund package page: http://www.bioconductor.org/packages...ummeRbund.html

[Baoqing]

ok, problem solved now.

I used one of the code you gave to other threads

sudo apt-get install libcurl4-openssl-dev

after installation, then reinstall it, now the biocLite("cummeRbund")
is loaded.

Thanks!

[Baoqing]

compiled info to install cummeRbund in ubuntu

wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz

tar xf R-2.15.0.tar.gz

sudo apt-get install xorg-dev

./configure

make

~/bin/R-2.15.0/bin

./R
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
# if the installation is not success, quit R and go back to ubuntu console
q()

sudo apt-get install libcurl4-openssl-dev

R

#Reinstall it
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

#then load the library, to see if all of the dependent packages are there
library(cummeRbund)

#change the directory of R
sudo rm -f ./R #after cd'ing to the directory containing the old version /usr/bin
sudo ln -s /path/to/new/R R #where R is an executable, not a directory

[jmwhitha]

Sorry I didn't get to this sooner. I just got back from Thailand.

[Baoqing]

Thats cool.

But I do have the following up question though. After load the library(CummeRbund). All of the dependents were loaded simultaneously. I would assume that the package is install properly. However, when i was trying to run the analysis.

> cuff_data = readCufflinks('diff_out')
> cuff_data
CuffSet instance with:
2 samples
5902 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
> csScatter(genes(cuff_data), '024', '025')
Error in .local(object, x, y, logMode, pseudocount, labels, smooth, ...) :
One or more values of 'x' or 'y' are not valid sample names!
Both instances are strange to me, because when I open the expression files. Those files are not empty(not necessarily mean not possible to have no isoforms or something else, how can i visually check the isoforms in the data sheet or TSS, etc, is there any thing specific labels with those?

Further more, when i was looking at the different expressed gene.
> gene_diff_data = diffData(genes(cuff_data))
> sig_gene_data = subset(gene_diff_data, (significant =='yes'))
> nrow(sig_gene_data)
[1] 0
This is certainly not the case, clearly in the result datasheet, dozens of genes have been listed as significant difference.

Best,