Question: I couldn't install DEseq2?
1
gravatar for enginbozaba
7 months ago by
enginbozaba0 wrote:

I did:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq")

I got the output and the installation

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘XML’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.19.tar.gz'
Content type 'application/x-gzip' length 1600788 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/annotate_1.58.0.tar.gz'
Content type 'application/x-gzip' length 1867576 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/genefilter_1.62.0.tar.gz'
Content type 'application/x-gzip' length 1432307 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/geneplotter_1.58.0.tar.gz'
Content type 'application/x-gzip' length 1428691 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DESeq2_1.20.0.tar.gz'
Content type 'application/x-gzip' length 2059356 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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/engin/R/x86_64-pc-linux-gnu-library/3.6/XML’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpnoZO5Z/downloaded_packages’
installation path not writeable, unable to update packages: boot, class,
  cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
  nnet, spatial, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status
> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("DESeq")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'DESeq'
also installing the dependencies ‘XML’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.19.tar.gz'
Content type 'application/x-gzip' length 1600788 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/annotate_1.62.0.tar.gz'
Content type 'application/x-gzip' length 1870418 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/genefilter_1.66.0.tar.gz'
Content type 'application/x-gzip' length 1419350 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/geneplotter_1.62.0.tar.gz'
Content type 'application/x-gzip' length 1435430 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq_1.36.0.tar.gz'
Content type 'application/x-gzip' length 1692053 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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/engin/R/x86_64-pc-linux-gnu-library/3.6/XML’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’
* removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/DESeq’

The downloaded source packages are in
    ‘/tmp/RtmpnoZO5Z/downloaded_packages’
installation path not writeable, unable to update packages: boot, class,
  cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
  nnet, spatial, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘DESeq’ had non-zero exit status
rna-seq R gene • 586 views
ADD COMMENTlink modified 7 months ago by RamRS25k • written 7 months ago by enginbozaba0
4
gravatar for RamRS
7 months ago by
RamRS25k
Houston, TX
RamRS25k wrote:

As the error message states, you're missing the package xml2-config. You can google how to install that (probably libxml2-dev) on your OS (if you're on Ubuntu/macOS, it should be easy with a package manager).

ADD COMMENTlink written 7 months ago by RamRS25k

As you said (sudo apt-get install libxml2 , sudo apt-get install libxml2-dev), the problem was solved. Thank you.:)

ADD REPLYlink modified 7 months ago by RamRS25k • written 7 months ago by enginbozaba0

https://image.ibb.co/dfsqrx/upvote_accept_bookmark.png

ADD REPLYlink written 7 months ago by ATpoint26k
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