Hello Friends

I am new in R and Bioconductor

I am installing the bioconducter packages the way its given in website but i am facing certain problem.

I am using Rstudio after installation certain software is not installed properly. the .tar.gz file is saved my folder. But when it comes to installation i get error :-

 installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib/R
checking for R... /usr/lib/R/bin/R
checking for R >= 3.1.0... yes
checking for cat... /bin/cat
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -E
configure: error: in `/tmp/RtmpnrVZio/R.INSTALL5f7d77ca0a7f/stringi':
configure: error: C preprocessor "g++ -E" fails sanity check
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/home/clevergene/R/x86_64-pc-linux-gnu-library/3.1/stringi’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Date.cpp -o Date.o
/bin/bash: g++: command not found
make: *** [Date.o] Error 127
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/clevergene/R/x86_64-pc-linux-gnu-library/3.1/Rcpp’
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c mclust.f -o mclust.o
/bin/bash: gfortran: command not found
make: *** [mclust.o] Error 127
ERROR: compilation failed for package ‘mclust’
* removing ‘/home/clevergene/R/x86_64-pc-linux-gnu-library/3.1/mclust’
* installing *source* package ‘quadprog’ ...
** package ‘quadprog’ successfully unpacked and MD5 sums checked
** libs
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c aind.f -o aind.o
/bin/bash: gfortran: command not found
make: *** [aind.o] Error 127
ERROR: compilation failed for package ‘quadprog’
* removing ‘/home/R/x86_64-pc-linux-gnu-library/3.1/quadprog’
* installing *source* package ‘affyio’ ...
checking for gcc... gcc
checking for C compiler default output file name... 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 grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for main in -lz... no
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs

I am using linux ubuntu 14.04LTS

please help me !!!!!!!!!!!

The error says it can't find gfortran, so:

sudo apt-get install gfortran

ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.2/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.2/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.2/DESeq’

what all software i need to install DEseq DESeq2 lumi bead array RQc?

please help !!!!!!!!!

When you facing with a dependency error problem, you can try to install the package that other packages depend on it. In your case, I guess is the annotate package. Then try to install only this package. An example:

library(BiocInstaller)
biocLite("annotate")

And see what is the error related to installation with this package. If this package depends on other package with error, try to install the other package. This is just a tip that I use when I am working with Bioconductor packages.

As you mentioned Rqc package in your question, the solution was commented by Mike Smith:

sudo apt-get install libxml2-dev libcurl4-gnutls-dev