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sekawaiwai2006
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@sekawaiwai2006-9531
Last seen 9.2 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")
Please update your question with the output of
biocLite("BSgenome").the error is simply"Error in library(BSgenome) : there is no package called ‘BSgenome’"
That is the output of the command
library(BSgenome). What is the output ofbiocLite("BSgenome")?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 statusthank you martin!
it is working fine now after i have used these two commands!