Hi everyone

I have tried to install DeSeq2 in R using R studio as well as ubuntu terminal but both doesnt succeed.

On R studio I can not find Deseq2 among the packages list. Rather It says

Warning in install.packages :
  package ‘deseq2’ is not available (for R version 3.4.2) 

On ubuntu

I use commands

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

and

biocLite("DESeq2")

Below is a long error which I says that it failed to install all 14 dependencies so failed to install Deseq2. Please help.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘GenomeInfoDb’, ‘XVector’, ‘DelayedArray’, ‘AnnotationDbi’, ‘annotate’, ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘genefilter’, ‘geneplotter’

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomeInfoDb_1.14.0.tar.gz'
Content type 'application/x-gzip' length 3402862 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/XVector_0.18.0.tar.gz'
Content type 'application/x-gzip' length 64711 bytes (63 KB)
==================================================
downloaded 63 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/DelayedArray_0.4.1.tar.gz'
Content type 'application/x-gzip' length 241117 bytes (235 KB)
==================================================
downloaded 235 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'
Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/annotate_1.56.2.tar.gz'
Content type 'application/x-gzip' length 1866282 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'
Content type 'application/x-gzip' length 432152 bytes (422 KB)
==================================================
downloaded 422 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'
Content type 'application/x-gzip' length 485066 bytes (473 KB)
==================================================
downloaded 473 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomicRanges_1.30.3.tar.gz'
Content type 'application/x-gzip' length 1116094 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/SummarizedExperiment_1.8.1.tar.gz'
Content type 'application/x-gzip' length 1204201 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
Content type 'application/x-gzip' length 43393 bytes (42 KB)
==================================================
downloaded 42 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Biobase_2.38.0.tar.gz'
Content type 'application/x-gzip' length 1656734 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/genefilter_1.60.0.tar.gz'
Content type 'application/x-gzip' length 1432282 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/geneplotter_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1428448 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/DESeq2_1.18.1.tar.gz'
Content type 'application/x-gzip' length 2139692 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error in apply_hotfix73465(getGeneric("cbind")) :
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/Biobase’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for package ‘IRanges’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/XVector’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘DelayedArray’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/DelayedArray’
ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘Biobase’, ‘BiocGenerics’ are not available for package ‘annotate’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/annotate’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘Biobase’, ‘DelayedArray’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘S4Vectors’, ‘AnnotationDbi’, ‘annotate’, ‘Biobase’ are not available for package ‘genefilter’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/genefilter’
ERROR: dependencies ‘Biobase’, ‘BiocGenerics’, ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/geneplotter’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmptBbVmU/downloaded_packages’
installation path not writeable, unable to update packages: XML, cluster,
  foreign, MASS, Matrix, mgcv, nlme, rpart, survival
Old packages: 'pillar'
Update all/some/none? [a/s/n]: a
also installing the dependency ‘fansi’

trying URL 'https://cran.rstudio.com/src/contrib/fansi_0.2.3.tar.gz'
Content type 'application/x-gzip' length 183361 bytes (179 KB)
==================================================
downloaded 179 KB

trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.3.0.tar.gz'
Content type 'application/x-gzip' length 103104 bytes (100 KB)
==================================================
downloaded 100 KB

* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c assumptions.c -o assumptions.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c has.c -o has.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nchar.c -o nchar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read.c -o read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rnchar.c -o rnchar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c state.c -o state.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strip.c -o strip.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strsplit.c -o strsplit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabs.c -o tabs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tohtml.c -o tohtml.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unhandled.c -o unhandled.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unique.c -o unique.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utf8.c -o utf8.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrap.c -o wrap.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fansi.so assumptions.o has.o init.o nchar.o read.o rnchar.o state.o strip.o strsplit.o tabs.o tohtml.o unhandled.o unique.o utf8.o utils.o wrap.o -L/usr/lib/R/lib -lR
installing to /home/musohail/R/x86_64-pc-linux-gnu-library/3.4/fansi/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fansi)
* installing *source* package ‘pillar’ ...
** package ‘pillar’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (pillar)

The downloaded source packages are in
    ‘/tmp/RtmptBbVmU/downloaded_packages’
There were 14 warnings (use warnings() to see them)