Unable to install DiffBind and DESeq2 4.0.3 and 4.0.4 (Package not available on these version of R error)

Question

[tiptophamza]

Hello,

Can anyone assist with how to I can install DiffBind and DESeq2 on the latest R version 4.0.4.

I have tried installing via the following means 1. source by downloading the source package (.tar.gz) on bio-conductor website

install.packages("~/Downloads/DESeq2_1.30.1.tar.gz", repos = NULL, type = "source")

1. Via BiocManager

   if (!requireNamespace("BiocManager", quietly = TRUE))

   • install.packages("BiocManager") > BiocManager::install("DiffBind")

2. install.packages(file.choose(), repos=NULL)

Thank you.

[MK]

I have similar problem when installing DESeq2.

Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

I have installed libcurl4-openssl-dev (it was already installed on my system). I don't understand part about: PATH and PKG_CONFIG_PATH. Everywhere I was looking for answer people assume you should know this. I would really appreciate if someone could explain me this.

[GenoMax]

See this post: https://stackoverflow.com/a/60878166

There is a link in it to a more detailed description of where the .pc file is installed. It is likely in /usr/lib/x86_64-linux-gnu/pkgconfig/libcurl.pc location.

[MK]

Thanks a lot for your answer. The link you've shared and checking some Linux basics helped me to solve the problem! I run:

#adding libcurl.pc file location to PATH and PKG_CONFIG_PATH
export PATH=/usr/lib/x86_64-linux-gnu/pkgconfig:$PATH
export PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig

After this I was able to install DESeq2 without errors.

NOTE: To make these changes permanent you need to add them to .bashrc

[tiptophamza]

Thank you for response @Kevin Blighe. Kindly find below the error messages for DESeq2, similar error was observed for DiffBind too.

> BiocManager::install('DESeq2')
Bioconductor version 3.12 (BiocManager
  1.30.10), R 4.0.4 (2021-02-15)
Installing package(s) 'DESeq2'
also installing the dependencies ‘curl’, ‘openssl’, ‘RCurl’, ‘XML’, ‘httr’, ‘GenomeInfoDb’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.tar.gz'
Content type 'application/x-gzip' length 673779 bytes (657 KB)
==================================================
downloaded 657 KB

trying URL 'https://cloud.r-project.org/src/contrib/openssl_1.4.3.tar.gz'
Content type 'application/x-gzip' length 1207708 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.3.tar.gz'
Content type 'application/x-gzip' length 728630 bytes (711 KB)
==================================================
downloaded 711 KB

trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.6.tar.gz'
Content type 'application/x-gzip' length 968773 bytes (946 KB)
==================================================
downloaded 946 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.2.tar.gz'
Content type 'application/x-gzip' length 159950 bytes (156 KB)
==================================================
downloaded 156 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/GenomeInfoDb_1.26.4.tar.gz'
Content type 'application/x-gzip' length 3453704 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/annotate_1.68.0.tar.gz'
Content type 'application/x-gzip' length 1872445 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/GenomicRanges_1.42.0.tar.gz'
Content type 'application/x-gzip' length 1175587 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/SummarizedExperiment_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1523133 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/genefilter_1.72.1.tar.gz'
Content type 'application/x-gzip' length 814755 bytes (795 KB)
==================================================
downloaded 795 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/geneplotter_1.68.0.tar.gz'
Content type 'application/x-gzip' length 1433556 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/DESeq2_1.30.1.tar.gz'
Content type 'application/x-gzip' length 2067936 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=

Answer 1

[Kevin Blighe]

The correct way to install is:

BiocManager::install('DESeq2')
BiocManager::install('DiffBind')

If these commands produce an error message (or messages), then please paste, here, the error message(s). Please also show the output of sessionInfo()

Kevin

[tiptophamza]

--------------------------- [ANTICONF] --------------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
    1 | #include <openssl/opensslv.h>
      |          ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/openssl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/RCurl’
* 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/mthamza/R/x86_64-pc-linux-gnu-library/4.0/XML’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/httr’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘httr’ are not available for package ‘annotate’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/SummarizedExperiment’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0/DESeq2’

The downloaded source packages are in
    ‘/tmp/Rtmp3gWou5/downloaded_packages’
There were 12 warnings (use warnings() to see them)
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils    
[5] datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.4     
[3] tools_4.0.4         tinytex_0.30       
[5] xfun_0.22          
> library(DESeq2)
Error in library(DESeq2) : there is no package called ‘DESeq2’

[Kevin Blighe]

Hi, you need to install some packages on your OS, i.e., outside of R. It seems that you would need to run, on Ubuntu:

sudo apt-get install libssl-dev
sudo apt-get install libcurl-dev

[tiptophamza]

Thank you Kevin...However, please note that the following error message was encountered after installing the dependency above.

> install.packages('DESeq2')
Installing package into ‘/home/mthamza/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘DESeq2’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

[MK]

Have a look here to check how to install DESeq2 https://bioinformatics.stackexchange.com/a/5581 (obviously change the R version to the current one)

In case you are not using anaconda, you can use bioconductor and type this in R:

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

BiocManager::install("DESeq2")