Problems installing DEseq on linux

reut · 03-31-2011, 03:05 AM

Hi
I'm trying to install R on a linux CentOS 5.5 with old R version - 2.8.1
I downloaded the DEseq .tar.gz and run R with these commands:

Code:

>source("http://bioconductor.org/biocLite.R")
>install.packages("locfit")
>install.packages("DESeq_1.3.3.tar.gz",repos=NULL)

* Installing *source* package 'DESeq' ...
** libs
gcc -I/usr/lib64/R/include  -I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c pval.c -o pval.o
gcc -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o DESeq.so pval.o   -L/usr/lib64/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6     2010-01-20
Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) :
  there is no package called 'genefilter'
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'DESeq'
** Removing '/usr/lib64/R/library/DESeq'
Warning message:
In install.packages("DESeq_1.3.3.tar.gz", repos = NULL) :
  installation of package 'DESeq_1.3.3.tar.gz' had non-zero exit status

the first time I did this, I got an error about Biobase package, so I installed it with install.packages, I also tried to install genefilter, but then it complains about another package...

Any suggestions?

colindaven · 03-31-2011, 03:28 AM

My experience is you should only install bioconductor packages on the latest version of R.

Simon Anders · 03-31-2011, 04:40 AM

If you install an R package manually, you need to make sure that you install all packages it depends on are available. If you look into DESeq's 'DESCRIPTION' file, you will see that it needs the following packages: genefilter, geneplotter, methods, Biobase, locfit

The 'biocLite' command (and the 'install.packages' command without 'repos=NULL') will take care of this for you.

DESeq might work on R 2.8, but if it doesn't, please update. It is Bioconductor policy to explicitly require users to keep their R up to date.

S

ecofriendly · 10-11-2011, 10:30 AM

Hi everyone,

Here's a technical question. I'm trying to use the newest version of DESeq (1.5.24, found here: http://bioconductor.org/packages/dev...tml/DESeq.html), because it would enable me to do a more complex contrast than the earlier version of DESeq.

This newest version of DESeq is compatible with Bioconductor 2.9 and the development version of R, 2.14. Yet I can't get the development version of R to compile properly (the pre-compiled version has not yet been released). I get the following error:

configure: error: --with-readline=yes (default) and headers/ libs are not available

Does anyone know how to solve this problem? Second, is there a way I can run the newest version of DESeq on the current R release, 2.13.2?

Thanks in advance,
Elena

tianyub836 · 10-11-2011, 07:35 PM

Quote:

Originally Posted by ecofriendly

Hi everyone,

Here's a technical question. I'm trying to use the newest version of DESeq (1.5.24, found here: http://bioconductor.org/packages/dev...tml/DESeq.html), because it would enable me to do a more complex contrast than the earlier version of DESeq.

This newest version of DESeq is compatible with Bioconductor 2.9 and the development version of R, 2.14. Yet I can't get the development version of R to compile properly (the pre-compiled version has not yet been released). I get the following error:

configure: error: --with-readline=yes (default) and headers/ libs are not available

Does anyone know how to solve this problem? Second, is there a way I can run the newest version of DESeq on the current R release, 2.13.2?

Thanks in advance,
Elena

well, that simple.

just inform you system administrator to install readline library

binlangman · 11-13-2014, 12:01 AM

I had run the following commands to install DESeq:

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

but there were some errors.

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'DESeq'
also installing the dependencies 'XML', 'annotate', 'genefilter', 'geneplotter'

试开URL’http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz'
Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb)
打开了URL
==================================================
downloaded 1.5 Mb

试开URL’http://bioconductor.org/packages/2.1..._1.40.1.tar.gz'
Content type 'application/x-gzip' length 1835494 bytes (1.8 Mb)
打开了URL
==================================================
downloaded 1.8 Mb

试开URL’http://bioconductor.org/packages/2.1..._1.44.0.tar.gz'
Content type 'application/x-gzip' length 1145312 bytes (1.1 Mb)
打开了URL
==================================================
downloaded 1.1 Mb

试开URL’http://bioconductor.org/packages/2.1..._1.40.0.tar.gz'
Content type 'application/x-gzip' length 1392637 bytes (1.3 Mb)
打开了URL
==================================================
downloaded 1.3 Mb

试开URL’http://bioconductor.org/packages/2.1..._1.14.0.tar.gz'
Content type 'application/x-gzip' length 1724530 bytes (1.6 Mb)
打开了URL
==================================================
downloaded 1.6 Mb

* installing *source* package 'XML' ...
** 成功将'XML'程序包解包并MD5和检查
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... /opt/illumina/HiSeqAnalysisSoftware/packages/bin/pkg-config
checking for xml2-config... /opt/illumina/HiSeqAnalysisSoftware/packages/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -r
Minor 8, Patch 0 for 2.8.0
Located parser file -I/illumina/development/Isis/packages/include/libxml2/parser.h
Checking for 1.8: -I/illumina/development/Isis/packages/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package 'XML'
* removing '/opt/R-3.0.2/lib64/R/library/XML'
ERROR: dependency 'XML' is not available for package 'annotate'
* removing '/opt/R-3.0.2/lib64/R/library/annotate'
ERROR: dependency 'annotate' is not available for package 'genefilter'
* removing '/opt/R-3.0.2/lib64/R/library/genefilter'
ERROR: dependency 'annotate' is not available for package 'geneplotter'
* removing '/opt/R-3.0.2/lib64/R/library/geneplotter'
ERROR: dependencies 'genefilter', 'geneplotter' are not available for package 'DESeq'
* removing '/opt/R-3.0.2/lib64/R/library/DESeq'

The downloaded source packages are in
'/tmp/RtmprhkjBa/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
警告信息：
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 'annotate' had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'genefilter' had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'geneplotter' had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'DESeq' had non-zero exit status

In this case, what shoud I do to install DESeq successfully?

Thanks!

dpryan · 11-13-2014, 12:38 AM

It looks like you have some sort of mismatch in the version of libxml you have installed. The error is complaining about mismatching versions of the library and header files...which would be unusual. See if you can find the aberrant file and remove it.

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11-13-2014, 12:01 AM	#6
binlangman Member Location: China Join Date: Dec 2013 Posts: 11	Errors when installing DESeq I had run the following commands to install DESeq: >source("http://bioconductor.org/biocLite.R") >biocLite("DESeq") but there were some errors. BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'DESeq' also installing the dependencies 'XML', 'annotate', 'genefilter', 'geneplotter' 试开URL’http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz' Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) 打开了URL ================================================== downloaded 1.5 Mb 试开URL’http://bioconductor.org/packages/2.1..._1.40.1.tar.gz' Content type 'application/x-gzip' length 1835494 bytes (1.8 Mb) 打开了URL ================================================== downloaded 1.8 Mb 试开URL’http://bioconductor.org/packages/2.1..._1.44.0.tar.gz' Content type 'application/x-gzip' length 1145312 bytes (1.1 Mb) 打开了URL ================================================== downloaded 1.1 Mb 试开URL’http://bioconductor.org/packages/2.1..._1.40.0.tar.gz' Content type 'application/x-gzip' length 1392637 bytes (1.3 Mb) 打开了URL ================================================== downloaded 1.3 Mb 试开URL’http://bioconductor.org/packages/2.1..._1.14.0.tar.gz' Content type 'application/x-gzip' length 1724530 bytes (1.6 Mb) 打开了URL ================================================== downloaded 1.6 Mb * installing source package 'XML' ... ** 成功将'XML'程序包解包并MD5和检查 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... /opt/illumina/HiSeqAnalysisSoftware/packages/bin/pkg-config checking for xml2-config... /opt/illumina/HiSeqAnalysisSoftware/packages/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -r Minor 8, Patch 0 for 2.8.0 Located parser file -I/illumina/development/Isis/packages/include/libxml2/parser.h Checking for 1.8: -I/illumina/development/Isis/packages/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default directories. ERROR: configuration failed for package 'XML' * removing '/opt/R-3.0.2/lib64/R/library/XML' ERROR: dependency 'XML' is not available for package 'annotate' * removing '/opt/R-3.0.2/lib64/R/library/annotate' ERROR: dependency 'annotate' is not available for package 'genefilter' * removing '/opt/R-3.0.2/lib64/R/library/genefilter' ERROR: dependency 'annotate' is not available for package 'geneplotter' * removing '/opt/R-3.0.2/lib64/R/library/geneplotter' ERROR: dependencies 'genefilter', 'geneplotter' are not available for package 'DESeq' * removing '/opt/R-3.0.2/lib64/R/library/DESeq' The downloaded source packages are in '/tmp/RtmprhkjBa/downloaded_packages' Updating HTML index of packages in '.Library' Making 'packages.html' ... done 警告信息： 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 'annotate' had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package 'genefilter' had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package 'geneplotter' had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package 'DESeq' had non-zero exit status In this case, what shoud I do to install DESeq successfully? Thanks!

03-31-2011, 03:28 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	My experience is you should only install bioconductor packages on the latest version of R.

03-31-2011, 04:40 AM	#3
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	If you install an R package manually, you need to make sure that you install all packages it depends on are available. If you look into DESeq's 'DESCRIPTION' file, you will see that it needs the following packages: genefilter, geneplotter, methods, Biobase, locfit The 'biocLite' command (and the 'install.packages' command without 'repos=NULL') will take care of this for you. DESeq might work on R 2.8, but if it doesn't, please update. It is Bioconductor policy to explicitly require users to keep their R up to date. S

10-11-2011, 10:30 AM	#4
ecofriendly Junior Member Location: University of Wisconsin, Madison Join Date: Nov 2010 Posts: 9	Hi everyone, Here's a technical question. I'm trying to use the newest version of DESeq (1.5.24, found here: http://bioconductor.org/packages/dev...tml/DESeq.html), because it would enable me to do a more complex contrast than the earlier version of DESeq. This newest version of DESeq is compatible with Bioconductor 2.9 and the development version of R, 2.14. Yet I can't get the development version of R to compile properly (the pre-compiled version has not yet been released). I get the following error: configure: error: --with-readline=yes (default) and headers/ libs are not available Does anyone know how to solve this problem? Second, is there a way I can run the newest version of DESeq on the current R release, 2.13.2? Thanks in advance, Elena

11-13-2014, 12:38 AM	#7
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	It looks like you have some sort of mismatch in the version of libxml you have installed. The error is complaining about mismatching versions of the library and header files...which would be unusual. See if you can find the aberrant file and remove it.