installing BSgenome and problems with XML and RCurl packages
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@sekawaiwai2006-9531
Last seen 5.3 years ago

Hello

i am trying to forge a BSgenome data package for Solanum pennellii, but i am not sure if i have installed the BSgenome package correctly because when i typed 

library("BSgenome") 

in the R terminal, i got an error "Error in library("BSgenome") : there is no package called ‘BSgenome’. " Does anyone know what is wrong??

the command i used to install BSgenome was the same in this link:

source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")
bsgenome • 1.2k views
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Please update your question with the output of biocLite("BSgenome").

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the error is simply"Error in library(BSgenome) : there is no package called ‘BSgenome’

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That is the output of the command library(BSgenome). What is the output of biocLite("BSgenome") ?

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the output is really long, i chose update all and using personal library for the questions being asked when installing, here is the out put:

> biocLite("BSgenome")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘BSgenome’
also installing the dependencies ‘XML’, ‘RCurl’, ‘rtracklayer’

trying URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.3.tar.gz'
Content type 'application/x-gzip' length 1607725 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://cran.rstudio.com/src/contrib/RCurl_1.95-4.7.tar.gz'
Content type 'application/x-gzip' length 916897 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/rtracklayer_1.30.1.tar.gz'
Content type 'application/x-gzip' length 1355877 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/BSgenome_1.38.0.tar.gz'
Content type 'application/x-gzip' length 6055101 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
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 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/yz2915/R/x86_64-pc-linux-gnu-library/3.2/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/BSgenome’

The downloaded source packages are in
	‘/tmp/RtmpmoPKSW/downloaded_packages’
Old packages: 'colorspace', 'digest', 'ggplot2', 'labeling', 'plyr', 'RColorBrewer', 'reshape2', 'scales', 'stringr', 'MASS', 'mgcv', 'spatial'
Update all/some/none? [a/s/n]: 
a
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  'lib = "/usr/lib/R/site-library"' is not writable
Would you like to use a personal library instead?  (y/n) y
trying URL 'http://cran.rstudio.com/src/contrib/colorspace_1.2-6.tar.gz'
Content type 'application/x-gzip' length 247027 bytes (241 KB)
==================================================
downloaded 241 KB

trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.9.tar.gz'
Content type 'application/x-gzip' length 116746 bytes (114 KB)
==================================================
downloaded 114 KB

trying URL 'http://cran.rstudio.com/src/contrib/ggplot2_2.0.0.tar.gz'
Content type 'application/x-gzip' length 1546130 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://cran.rstudio.com/src/contrib/labeling_0.3.tar.gz'
Content type 'application/x-gzip' length 10722 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'http://cran.rstudio.com/src/contrib/plyr_1.8.3.tar.gz'
Content type 'application/x-gzip' length 392337 bytes (383 KB)
==================================================
downloaded 383 KB

trying URL 'http://cran.rstudio.com/src/contrib/RColorBrewer_1.1-2.tar.gz'
Content type 'application/x-gzip' length 11532 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'http://cran.rstudio.com/src/contrib/reshape2_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34693 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'http://cran.rstudio.com/src/contrib/scales_0.3.0.tar.gz'
Content type 'application/x-gzip' length 57030 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://cran.rstudio.com/src/contrib/stringr_1.0.0.tar.gz'
Content type 'application/x-gzip' length 34880 bytes (34 KB)
==================================================
downloaded 34 KB

* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** libs
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 colorspace.c -o colorspace.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o colorspace.so colorspace.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘colorspace’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (colorspace)
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
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 aes.c -o aes.o
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 crc32.c -o crc32.o
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 digest.c -o digest.o
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 init.c -o init.o
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 md5.c -o md5.o
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 pmurhash.c -o pmurhash.o
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 raes.c -o raes.o
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 sha1.c -o sha1.o
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 sha2.c -o sha2.o
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 sha256.c -o sha256.o
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 xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/digest/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (digest)
* installing *source* package ‘labeling’ ...
** package ‘labeling’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (labeling)
* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c loop_apply.c -o loop_apply.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c split-numeric.cpp -o split-numeric.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o plyr.so RcppExports.o loop_apply.o split-numeric.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/plyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plyr)
* installing *source* package ‘RColorBrewer’ ...
** package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RColorBrewer)
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (stringr)
* installing *source* package ‘reshape2’ ...
** package ‘reshape2’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c melt.cpp -o melt.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o reshape2.so RcppExports.o melt.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/reshape2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (reshape2)
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c colors.cpp -o colors.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o scales.so RcppExports.o colors.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/scales/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (scales)
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)

The downloaded source packages are in
	‘/tmp/RtmpmoPKSW/downloaded_packages’
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  'lib = "/usr/lib/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) y
trying URL 'http://cran.rstudio.com/src/contrib/MASS_7.3-45.tar.gz'
Content type 'application/x-gzip' length 487555 bytes (476 KB)
==================================================
downloaded 476 KB

trying URL 'http://cran.rstudio.com/src/contrib/mgcv_1.8-10.tar.gz'
Content type 'application/x-gzip' length 802060 bytes (783 KB)
==================================================
downloaded 783 KB

trying URL 'http://cran.rstudio.com/src/contrib/spatial_7.3-11.tar.gz'
Content type 'application/x-gzip' length 44666 bytes (43 KB)
==================================================
downloaded 43 KB

* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** libs
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 MASS.c -o MASS.o
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 lqs.c -o lqs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/MASS/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 (MASS)
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c coxph.c -o coxph.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c discrete.c -o discrete.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c gdi.c -o gdi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c magic.c -o magic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mat.c -o mat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c misc.c -o misc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mvn.c -o mvn.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c qp.c -o qp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c soap.c -o soap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mgcv.so coxph.o discrete.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 -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/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)
* installing *source* package ‘spatial’ ...
** package ‘spatial’ successfully unpacked and MD5 sums checked
** libs
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 init.c -o init.o
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 krc.c -o krc.o
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 pps.c -o pps.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o spatial.so init.o krc.o pps.o -L/usr/lib/R/lib -lR
installing to /home/yz2915/R/x86_64-pc-linux-gnu-library/3.2/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (spatial)

The downloaded source packages are in
	‘/tmp/RtmpmoPKSW/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
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Entering edit mode

thank you martin!

it is working fine now after i have used these two commands!

sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libxml2-dev
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Entering edit mode
@martin-morgan-1513
Last seen 2 days ago
United States

Thanks! It's better to edit the original question and to post a comment indicating that you've made the change, otherwise we get narrower and narrower...

Note that the XML and RCurl package installations fail. For XML we see

checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’

and for RCurl

** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’

The XML and RCurl packages have system software dependencies. You need to install the 'dev' version of the xml2 and curl libraries; on my OS (Ubuntu 14.04.3 LTS -- I should have asked you to paste  the output of the sessionInfo() command too!) I would do this with

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

The rtracklayer and BSgenome packages also fail to install, but this is because the XML and RCurl dependencies failed.

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