packages installation problem
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@rayagirish-9685
Last seen 4.0 years ago

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 !!!!!!!!!!!

 

limma Rqc beadarray Lumi • 5.0k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 18 months ago
United States

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

sudo apt-get install gfortran

 

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1
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It also looks like g++ is missing, so I'd suggest running this as well:

sudo apt-get install build-essential

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after build essential also the same error is repeated.

What all system requirement is there for instaling DEseq DESeq 2 RQC lumi beadarray

thanks

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thanks

why this error come when i need to download biostring

io_utils.c -o io_utils.o
io_utils.c:16:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
                  ^
compilation terminated.
make: *** [io_utils.o] Error 1
ERROR: compilation failed for package ‘Biostrings’

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Because the system dependency zlib.h is not found; googling for 'zlib.h: No such file or directory' would have helped. On a linux system this would be unusual, but could be addressed as Dan indicated by installing the relevant system dependency sudo apt-get installl zlib1g-dev.

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@rayagirish-9685
Last seen 4.0 years ago
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 !!!!!!!!!

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gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c simul.c -o simul.o

and what is the meaning of this type of error??

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1
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That doesn't look like an error to me, that's just the output of the gcc C compiler.

It looks like the 'annotate' package depends on XML (and maybe Curl).  I would install the developmental libraries for these as well as zlib, gcc, gfortran etc.

sudo apt-get install libcurl4-gnutls-dev libxml2-dev zlib1g-dev

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@wdesouza
Last seen 21 months ago
Brazil

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
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there are certain packages depending on X11 for my ubuntu system i tried searching it on net. what i got in internet is to download :-

sudo apt-get install xorg openbox
sudo apt-get install xorg
sudo apt-get install openbox

after upgrading my system still there are certain software which are dpending on  X11

and error i get is no X11 is found

can any one help me out from this

package which is was installing was lumi

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this is error:

configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’

lumi is depended on certain packages like rgl , mixomic and minfi

please help

thank you

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It's worth baring in mind that whenever you encounter the 'filling missing: blah.h' style errors, you almost certainly want to install the development versions of the packages in Ubuntu.  These usually end with '-dev'.  So you want xorg-dev.

The rgl package has a README with instructions for installing the various dependencies on a variety of systems.  You can read it here:

https://cran.r-project.org/web/packages/rgl/README

Often packages that require specific system libraries will detail them either in a README or the package vignette.  In your case I would run the following:

sudo apt-get install xorg-dev libgl1-mesa-dev libglu1-mesa-dev
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