Error in find DEXSeq package
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@engryahya602-7735
Last seen 5.9 years ago
Pakistan

i downloaded the DEXSeq using these commands

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

aftere downloading is finished i  typed

browseVignettes("DEXSeq")

but it gives an error

Error in find.package(package, lib.loc) :
  there is no package called ‘DEXSeq’


can any one tell me how to fix this???

deseq dexseq • 2.0k views
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Did it get installed correctly?

what version of R/DEXSeq are you using?

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R is 3.1.1..i followed this link to install DEXSEQ         

http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html

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but did it install correctly?

try to re-install it.

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yes it was  installed correctly...there were just warnings no erros after completion

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This is what I'm getting, when I am installing DEXSeq:

> library(BiocInstaller)
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help

> biocLite("DEXSeq")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘DEXSeq’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/DEXSeq_1.14.0.tgz'
Content type 'application/x-gzip' length 517702 bytes (505 KB)
==================================================
downloaded 505 KB


What kind of warning do you see?

Did you try to re-install it?

 

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let me re install it and i will attach the snapshot then..

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this was first warning..what should i do now???
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  'lib = "/usr/local/lib/R/library"' is not writable
Would you like to use a personal library instead?  (y/n)

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you can answer yes or just y

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these  are last few lines

installing to /home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)

The downloaded source packages are in
    ‘/tmp/RtmpTJ181T/downloaded_packages’
> browseVignettes("DEXSeq")
Error in find.package(package, lib.loc) :
  there is no package called ‘DEXSeq’

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these  are last few lines

installing to /home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)

The downloaded source packages are in
    ‘/tmp/RtmpTJ181T/downloaded_packages’
> browseVignettes("DEXSeq")
Error in find.package(package, lib.loc) :
  there is no package called ‘DEXSeq’

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this is not the DEXSeq package.

As the last line says - * DONE (mgcv)

where is the installation of DEXSeq?

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what should i do now?? i follow that link for installation and these are last lines..can you help me out how to install it ?

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copy paste all the lines

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all lines after completion ???

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all the lines from

> install.packages("DEXSeq")

 

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Installing package into ‘/home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
Warning message:
package ‘DEXSeq’ is not available (for R version 3.1.1)

 

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First - is that all?

second - Do

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

 

Try it with that and try again to install the package.

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Using install.packages() is not correct for Bioconductor packages. Please use

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

and provide ALL the output.

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true my mistake.

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i could copy only these lines

ITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o
make[2]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/CHOLMOD'
make[1]: Entering directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/COLAMD'
( cd Source ; make lib )
make[2]: Entering directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/COLAMD/Source'
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -c colamd_global.c -o colamd_global.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -c colamd.c -o colamd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[2]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/COLAMD/Source'
make[1]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/COLAMD'
make[1]: Entering directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/AMD'
( cd Source ; make lib )
make[2]: Entering directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/AMD/Source'
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -g -O2  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o
make[2]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/AMD/Source'
make[1]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/AMD'
make[1]: Entering directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DNTIMER -I/usr/local/include    -fpic  -g -O2  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[1]: Leaving directory `/tmp/RtmpKF82Ua/R.INSTALL10d930179f10/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/usr/local/lib -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘crossprod’ in package ‘Matrix’
Creating a new generic function for ‘tcrossprod’ in package ‘Matrix’
Creating a generic function for ‘image’ from package ‘graphics’ in package ‘Matrix’
Creating a generic function for ‘solve’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘chol2inv’ from ‘base’ in package ‘Matrix’
    (from the saved implicit definition)
Creating a generic function for ‘chol2inv’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘determinant’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘update’ from package ‘stats’ in package ‘Matrix’
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘t’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘as.array’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Matrix’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘Matrix’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘Matrix’
Creating a generic function for ‘isSymmetric’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘unname’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘chol’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rcond’ from ‘base’ in package ‘Matrix’
    (from the saved implicit definition)
Creating a generic function for ‘rcond’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘all.equal’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘Matrix’
in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"dsparseMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csr","dgCMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","dgCMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csr","RsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","CsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","TsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","Matrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","Matrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","Matrix"’: no definition for class “matrix.csc”
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Matrix’
in method for ‘colSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘rowSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘colMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘rowMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
Creating a generic function for ‘zapsmall’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘print’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘which’ from package ‘base’ in package ‘Matrix’
in method for ‘coerce’ with signature ‘"graphAM","sparseMatrix"’: no definition for class “graphAM”
in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","Matrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graphNEL","CsparseMatrix"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"sparseMatrix","graph"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"sparseMatrix","graphNEL"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: no definition for class “graphNEL”
Creating a generic function for ‘format’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.R’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.Q’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qy’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qty’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.coef’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.resid’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.fitted’ from package ‘base’ in package ‘Matrix’
** help
*** installing help indices
** building package indices
Loading required package: Matrix

Attaching package: ‘Matrix’

The following objects are masked from ‘package:base’:

    crossprod, tcrossprod

** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2  -c chol.f -o chol.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c corStruct.c -o corStruct.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c gnls.c -o gnls.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nlme.c -o nlme.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nlmefit.c -o nlmefit.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nls.c -o nls.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c pdMat.c -o pdMat.o
gfortran   -fpic  -g -O2  -c rs.f -o rs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran -lm -lquadmath
installing to /home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c coxph.c -o coxph.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c gdi.c -o gdi.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c magic.c -o magic.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c mat.c -o mat.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c misc.c -o misc.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c mvn.c -o mvn.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c qp.c -o qp.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c soap.c -o soap.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o mgcv.so coxph.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
installing to /home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)

The downloaded source packages are in
    ‘/tmp/RtmpCfVY09/downloaded_packages’
There were 14 warnings (use warnings() to see them)
 -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.olude    -fpic  -g -O2  
Error: unexpected symbol in "browseVignettes("DEXSeq")ITION"
lmod_write.c -o cholmod_l_write.olude    -fpic  -g -O2  -DDLONG -c  ../Check/cho
Error: unexpected symbol in "ITION -DNPRINT -I/usr/local/include    -fpic  -g -O2  -DDLONG -c  .."

 

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Entering edit mode

I'm using this level of comment to avoid very short lines.

It seems that you installed a number of packages. Most were successful. So try biocLite("DEXSeq") again, and it should attempt to only install a few packages. If possible, try to narrow down to the first package that fails to install. Report the output of the failed package installation here.

This

Error: unexpected symbol in "browseVignettes("DEXSeq")ITION"

is completely unexpected. Where did it come from? Do you have a file .Rdata in the directory returned by getwd()

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yes i think i pressed some button unintentionally but after installation..i will try biocLite("DEXSeq") again and will post the error

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Entering edit mode

This was error

> biocLite("DEXSeq")
Error: could not find function "biocLite"

 

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0
Entering edit mode

have you sourced the file:

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

or try to install the package BiocInstaller:

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

It will be a lot easier if you do all this steps in one go and than post here ALL the commands and the results together, so we can follow your output.

"pressed some buttons" is not an error one can work with.

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Sorry for the inconvenience ...this was output after all the steps

* installing *source* package ‘RCurl’ ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/RCurl’
Error in untar2(tarfile, files, list, exdir, restore_times) :
  incomplete block on file
ERROR: dependency ‘BatchJobs’ is not available for package ‘BiocParallel’
* removing ‘/home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/BiocParallel’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/home/bioinformatics/R/x86_64-unknown-linux-gnu-library/3.1/biomaRt’
Error in untar2(tarfile, files, list, exdir, restore_times) :
  incomplete block on file
Error in untar2(tarfile, files, list, exdir, restore_times) :
  incomplete block on file
Error in untar2(tarfile, files, list, exdir, restore_times) :
  incomplete block on file

The downloaded source packages are in
    ‘/tmp/Rtmpk3DrEZ/downloaded_packages’
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 239693 != reported length 1396205
2: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 921943 != reported length 1150612
3: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 106759 != reported length 373961
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘BiocParallel’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘genefilter’ had non-zero exit status
10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘DEXSeq’ had non-zero exit status

 

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Entering edit mode

Start with the first package that fails to load -- RCurl. The problem is likely that you are missing a system dependency, the 'devel' version of libcurl. Likely you are missing the system dependency for XML, too, the 'devel' version of libxml2. See for instance James MacDonald's reply to Problems to install a package - Ubuntu.

The 'untar' and 'download.file' error messages suggest that you had difficulty during package download. This is quite unusual. I guess you have a poor internet connection. The only solution I know of is to 'try again', maybe separately for each problem package.

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yes you are right..internet connection is poor..how to install each one separately ?

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0
Entering edit mode

Maybe you can try and download the packages manually from the browser and than install them locally and not from the repository.

This way you can see in advance, if the files was downloaded completely, or not.

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0
Entering edit mode

biocLite("BiocInstaller")  does not do anything useful in this case; the BiocInstaller package has already been installed by source(...).

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0
Entering edit mode

if you say so...

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Entering edit mode

Thanks to both of you..i solved it by upgrading the R to latest version..now it is installed

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