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Old 06-27-2013, 06:34 PM   #41
BioSlayer
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Default How I solved it

I just upgraded to Ubuntu 12 and together with it an updated version of R was installed. I faced an issue regarding the availability of cummeRbund for the earlier version of Ubuntu and this is why I did the upgrade.

However, I faced a similar issue to the situation you describe. A complaint about RCurl not being configurable and that curl-config wasn't found. So I basically run this command on the terminal
Code:
ERROR: configuration failed for package 'RCurl'
then moved to R shell
Code:
sudo R
source(http://bioconductor.org/biocLite.R)
biocLite("cummeRbund");
biocLite() then should be able to install all the packages and dependencies required for cummeRbund as well as update older ones.
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Old 06-27-2013, 11:10 PM   #42
bio_jit
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Unhappy cummeRbund installtion problem

Hi all

I am a new in this subject and trying to install cummeRbund but failed. I tryed all the instruction given here before but I am facing a bit different prob. Here I am sending you my probs plz. send me a solution

I am using fedora 16 32bit, R 2.15.2, Bioconductor 2.11


trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/cummeRbund_2.0.0.tar.gz'
Content type 'application/x-gzip' length 2327551 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/lib/R/library/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/usr/lib/R/library/biomaRt’
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/usr/lib/R/library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/lib/R/library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/usr/lib/R/library/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/usr/lib/R/library/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/lib/R/library/cummeRbund’

The downloaded source packages are in
‘/tmp/RtmpRFghP0/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 ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biomaRt’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status

As per previous instruction i read in this forum I installed "libcurl"

Dependencies Resolved

===========================================================================================================================================
Package Arch Version Repository Size
===========================================================================================================================================
Installing:
libcurl-devel i686 7.21.7-8.fc16 updates 276 k

Transaction Summary
===========================================================================================================================================
Install 1 Package

Total download size: 276 k
Installed size: 570 k
Is this ok [y/N]: y
Downloading Packages:
libcurl-devel-7.21.7-8.fc16.i686.rpm | 276 kB 00:04
Running Transaction Check
Running Transaction Test
Transaction Test Succeeded
Running Transaction
Installing : libcurl-devel-7.21.7-8.fc16.i686 1/1
Verifying : libcurl-devel-7.21.7-8.fc16.i686 1/1

Installed:
libcurl-devel.i686 0:7.21.7-8.fc16

Complete!

Now I check if the installation is o.k or not by

which xml2-configure
/usr/bin/which: no xml2-configure in (/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/avrajit/.local/bin:/home/avrajit/bin)

plz. guide me out from this i need to run cummeRbund
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Old 08-07-2013, 11:09 PM   #43
jp.
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Question

Can anybody tell me, if I can install cummeRbund on my user account (linux server) without root permision. R is installed in root and can be accessed from every user but not cummeRbund. I want to install cummeRbund within my user area ?
anybody has done like this ?
expecting replies ?
Thank you
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Old 10-30-2013, 04:33 AM   #44
yincf
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Default Xml

dear GenoMax,
Maybe I have got an new problem of a different error:
please help!

/usr/bin/ld: /usr/local/lib/libxml2.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libxml2.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [XML.so] Error 1
ERROR: compilation failed for package ‘XML’
* removing ‘/usr/local/lib64/R/library/XML’
ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
* removing ‘/usr/local/lib64/R/library/biomaRt’
ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’
* removing ‘/usr/local/lib64/R/library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib64/R/library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/usr/local/lib64/R/library/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/usr/local/lib64/R/library/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/local/lib64/R/library/cummeRbund’
The downloaded source packages are in
‘/tmp/RtmpDzK6OA/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 ‘biomaRt’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status
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Old 10-30-2013, 05:06 AM   #45
GenoMax
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Have you installed libxml2 library (this is ubuntu I assume)?
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Old 10-30-2013, 09:26 PM   #46
yincf
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Default Thanks GenoMax!

Quote:
Originally Posted by GenoMax View Post
Have you installed libxml2 library (this is ubuntu I assume)?
Thank you very much for your kindly response! I have installed libxml2 library and also tried to install XML-3.98 alone but get Error2/3. My 64bit-PC is lying on Ubuntu 12.04 LTS system.

Error2: install XML alone
$ cd XML
$ sh ./configure --host=x86_64
......
Minor 9, Patch 1 for 2.9.1
Located parser file -I/usr/local/include/libxml2/parser.h
Checking for 1.8: -I/usr/local/include/libxml2
Using libxml2.*
checking for gzopen in -lz... no
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"

Error3: install XML in R
>install.package("XML")
.......
/usr/bin/ld: /usr/local/lib/libxml2.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libxml2.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [XML.so] Error 1
ERROR: compilation failed for package ‘XML’
* removing ‘/usr/local/lib64/R/library/XML’
The downloaded source packages are in
‘/tmp/RtmpsOfYSc/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("XML") :
installation of package ‘XML’ had non-zero exit status

Libxml2:
$ sudo apt-get install libxml2
Reading package lists... Done
Building dependency tree
Reading state information... Done
libxml2 is already the newest version.
The following packages were automatically installed and are no longer required:
natefoo-taxonomy python-numexpr tk-table python-gnuplot libhdf5-serial-1.8.4
liblzo2-2 natefoo-add-scores galaxy-server-test python-tables macs14
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 569 not upgraded.
$ which xml2-config
/usr/local/bin/xml2-config

Last edited by yincf; 10-31-2013 at 03:20 AM.
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Old 10-31-2013, 03:01 AM   #47
GenoMax
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Do you have zlib1g and zlib1g-dev installed?
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Old 10-31-2013, 07:56 AM   #48
yincf
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Quote:
Originally Posted by GenoMax View Post
Do you have zlib1g and zlib1g-dev installed?
I have installed them, but the error changed nothing!

Thank you!
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Old 10-31-2013, 08:02 AM   #49
Kerah
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Default error installing cummerbund on windows7

Hello all,
I am also having issues finishing the cummerbund installation too, but I'm using a windows7 starter netbook computer.

These first 2 commands work fine:
> source('http://www.bioconductor.org/biocLite.R')
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'cummeRbund'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/cummeRbund_2.4.0.zip'
Content type 'application/zip' length 2601827 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

But when I try to load the cummerbund library I get the following errors
> library(cummeRbund)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘biomaRt’
Error: package ‘Gviz’ could not be loaded

I've tried installing these packages alone but that does not work either and cummerbund does not work without them. (see below)
> install.packages('biomaRt')
package ‘biomaRt’ is not available (for R version 3.0.2)
> install.packages('Gviz')
Warning message:
package ‘Gviz’ is not available (for R version 3.0.2)

> cuff<-readCufflinks()
Error: could not find function "readCufflinks"

Please help me if you know how to fix this issue.
Thanks
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Old 10-31-2013, 09:20 AM   #50
GenoMax
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Default

Quote:
Originally Posted by yincf View Post
I have installed them, but the error changed nothing!

Thank you!

Looking at your last message it appears that you only posted error 2 and 3. What was error 1? Can you post that?
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Old 10-31-2013, 09:24 AM   #51
GenoMax
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Default

Quote:
Originally Posted by Kerah View Post
Hello all,
I am also having issues finishing the cummerbund installation too, but I'm using a windows7 starter netbook computer.

These first 2 commands work fine:
> source('http://www.bioconductor.org/biocLite.R')
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'cummeRbund'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/cummeRbund_2.4.0.zip'
Content type 'application/zip' length 2601827 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

But when I try to load the cummerbund library I get the following errors
> library(cummeRbund)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘biomaRt’
Error: package ‘Gviz’ could not be loaded

I've tried installing these packages alone but that does not work either and cummerbund does not work without them. (see below)
> install.packages('biomaRt')
package ‘biomaRt’ is not available (for R version 3.0.2)
> install.packages('Gviz')
Warning message:
package ‘Gviz’ is not available (for R version 3.0.2)

> cuff<-readCufflinks()
Error: could not find function "readCufflinks"

Please help me if you know how to fix this issue.
Thanks
Did you try?
Code:
source("http://bioconductor.org/biocLite.R")
biocLite("Gviz")
biocLite("biomaRt")
Are you installing in cygwin?
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Old 10-31-2013, 11:51 AM   #52
Kerah
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Thumbs up

Quote:
Originally Posted by GenoMax View Post
Did you try?
Code:
source("http://bioconductor.org/biocLite.R")
biocLite("Gviz")
biocLite("biomaRt")
Are you installing in cygwin?
Wow thank you so much GenoMax that worked like a charm!
CummeRbund is up and running and I can make plots from the data.
Many thanks
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Old 10-31-2013, 09:49 PM   #53
yincf
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Quote:
Originally Posted by GenoMax View Post
Looking at your last message it appears that you only posted error 2 and 3. What was error 1? Can you post that?
Thanks again!
I am sorry the number of errors may not be exact. Error 1 is the first information I have posted in this topic.
Now I guess that my problem is XML installation, but I can not fix it.
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Old 11-01-2013, 03:23 AM   #54
GenoMax
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Quote:
Originally Posted by yincf View Post
Thanks again!
I am sorry the number of errors may not be exact. Error 1 is the first information I have posted in this topic.
Now I guess that my problem is XML installation, but I can not fix it.
Can you tell me what version of R you are using?

One of the things that may be useful to try is to upgrade R to the latest version using the directions at this link: http://korolevbin.blogspot.com/2013/...on-ubuntu.html
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Old 11-01-2013, 10:12 PM   #55
yincf
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Default Thankyou

Quote:
Originally Posted by GenoMax View Post
Can you tell me what version of R you are using?

One of the things that may be useful to try is to upgrade R to the latest version using the directions at this link: http://korolevbin.blogspot.com/2013/...on-ubuntu.html
Thank you very much GenoMax, you are realy my god!
My cummeRbund is ok now! I reinstalled R-3.0.2 and libxml2 with source.
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Old 12-01-2013, 05:44 PM   #56
reco
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Arrow Hmisc installation error when installing cummeRbund

I am receiving this error while installing cummeRbund on Ubuntu 12.04 LTS using the biocLite. The following error makes little sense to me, only that it should be something to do with the compilation of Hmisc source. Running as a root didn't solve my problem; the trail is also given below.

/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package ‘Hmisc’


Trail:

[email protected]:~$ sudo -s
[email protected]:~# R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'cummeRbund'
also installing the dependencies ‘Hmisc’, ‘biovizBase’, ‘Gviz’

trying URL 'http://cran.fhcrc.org/src/contrib/Hmisc_3.13-0.tar.gz'
Content type 'application/x-gzip' length 587751 bytes (573 Kb)
opened URL
==================================================
downloaded 573 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/biovizBase_1.10.5.tar.gz'
Content type 'application/x-gzip' length 1036027 bytes (1011 Kb)
opened URL
==================================================
downloaded 1011 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Gviz_1.6.0.tar.gz'
Content type 'application/x-gzip' length 1965136 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/cummeRbund_2.4.0.tar.gz'
Content type 'application/x-gzip' length 2273576 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb

* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c Hmisc.c -o Hmisc.o
gfortran -fpic -O3 -pipe -g -c cidxcn.f -o cidxcn.o
gfortran -fpic -O3 -pipe -g -c cidxcp.f -o cidxcp.o
gfortran -fpic -O3 -pipe -g -c hoeffd.f -o hoeffd.o
gfortran -fpic -O3 -pipe -g -c jacklins.f -o jacklins.o
gfortran -fpic -O3 -pipe -g -c largrec.f -o largrec.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c mChoice.c -o mChoice.o
gfortran -fpic -O3 -pipe -g -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c nstr.c -o nstr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c ranksort.c -o ranksort.o
gfortran -fpic -O3 -pipe -g -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c string_box.c -o string_box.o
gfortran -fpic -O3 -pipe -g -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/Hmisc’
ERROR: dependency ‘Hmisc’ is not available for package ‘biovizBase’
* removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/biovizBase’
ERROR: dependency ‘biovizBase’ is not available for package ‘Gviz’
* removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/Gviz’
ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’
* removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/cummeRbund’

The downloaded source packages are in
‘/tmp/Rtmpt64xmr/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Hmisc’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status

Please help. Thanks.
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Old 12-02-2013, 03:03 AM   #57
GenoMax
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See answer #2 or 3 in this thread: http://stackoverflow.com/questions/6...find-lgfortran

One of those should work for you.
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Old 12-02-2013, 05:03 AM   #58
reco
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Quote:
Originally Posted by GenoMax View Post
See answer #2 or 3 in this thread: http://stackoverflow.com/questions/6...find-lgfortran

One of those should work for you.
GenoMax, this solved the problem. Thank you.

The problem was due to the missing link in /usr/lib/libfortran.so on my Ubuntu 12.04 LTS.

So this corrected it,

sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so
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Old 12-13-2013, 01:44 PM   #59
mhkiani
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I have got my results from cuffdiff and just wondering that what would be the best option to visualize the data?
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Old 12-15-2013, 07:31 PM   #60
jp.
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Wink

library(cummeRbund)

good luck
jp.


Quote:
Originally Posted by mhkiani View Post
I have got my results from cuffdiff and just wondering that what would be the best option to visualize the data?
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