Question: problem when try to install GenomicFeatures packages
0
gravatar for Changbin Du
9.4 years ago by
Changbin Du10
Changbin Du10 wrote:
HI, Dear, I am a biginner of BIOconductor. When I try to install the GenomicFeatures package, I failed two times. Here is the code in R under Linux: > biocLite("GenomicFeatures.Hsapiens.UCSC.hg18") Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "GenomicFeatures.Hsapiens.UCSC.hg18" Please wait... also installing the dependencies ?RCurl?, ?rtracklayer?, ?GenomicFeatures? trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-1.tar.gz' Content type 'application/x-gzip' length 800529 bytes (781 Kb) opened URL ================================================== downloaded 781 Kb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/rtracklayer _1.6.0.tar.gz' Content type 'application/x-gzip' length 1363174 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GenomicFeat ures_0.2.0.tar.gz' Content type 'application/x-gzip' length 70108 bytes (68 Kb) opened URL ================================================== downloaded 68 Kb trying URL 'http://www.bioconductor.org/packages/2.5/data/experiment/src/contrib/ GenomicFeatures.Hsapiens.UCSC.hg18_0.1.1.tar.gz' Content type 'application/x-gzip' length 19774391 bytes (18.9 Mb) opened URL ================================================== downloaded 18.9 Mb * installing *source* package ?RCurl? ... checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ?RCurl? * removing ?/home/cdu/library/RCurl? * installing *source* package ?rtracklayer? ... ** R ** data ** demo ** inst ** preparing package for lazy loading Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'RCurl' Error : package 'RCurl' could not be loaded ERROR: lazy loading failed for package ?rtracklayer? * removing ?/home/cdu/library/rtracklayer? * installing *source* package ?GenomicFeatures? ... ** R ** inst ** preparing package for lazy loading Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'rtracklayer' Error : package 'rtracklayer' could not be loaded ERROR: lazy loading failed for package ?GenomicFeatures? * removing ?/home/cdu/library/GenomicFeatures? * installing *source* package ?GenomicFeatures.Hsapiens.UCSC.hg18? ... ** R ** inst ** preparing package for lazy loading Error : package 'GenomicFeatures' required by 'GenomicFeatures.Hsapiens.UCSC.hg18' could not be found ERROR: lazy loading failed for package ?GenomicFeatures.Hsapiens.UCSC.hg18? * removing ?/home/cdu/library/GenomicFeatures.Hsapiens.UCSC.hg18? The downloaded packages are in ?/tmp/Rtmp26fOPJ/downloaded_packages? Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'RCurl' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'rtracklayer' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'GenomicFeatures' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'GenomicFeatures.Hsapiens.UCSC.hg18' had non-zero exit status Can you help me with this? Thanks! -- Sincerely, Changbin -- Changbin Du DOE Joint Genome Institute Bldg 400 Rm 457 2800 Mitchell Dr, Walnut Creet, CA 94598 Phone: 925-927-2856 Fax: 925-296-5850
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ADD COMMENTlink modified 9.4 years ago by Chao-Jen Wong580 • written 9.4 years ago by Changbin Du10
Answer: problem when try to install GenomicFeatures packages
0
gravatar for Kasper Daniel Hansen
9.4 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
You need curl. I assume you are under linux. Ask you sysadmin to install curl and curl-devel Kasper On Jan 7, 2010, at 20:23 PM, Changbin Du wrote: > HI, Dear, > > I am a biginner of BIOconductor. When I try to install the GenomicFeatures package, I failed two times. Here is the code in R under Linux: > > > biocLite("GenomicFeatures.Hsapiens.UCSC.hg18") > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "GenomicFeatures.Hsapiens.UCSC.hg18" > Please wait... > > also installing the dependencies ?RCurl?, ?rtracklayer?, ?GenomicFeatures? > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-1.tar.gz' > Content type 'application/x-gzip' length 800529 bytes (781 Kb) > opened URL > ================================================== > downloaded 781 Kb > > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/rtracklayer_1.6.0.tar.gz' > Content type 'application/x-gzip' length 1363174 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/GenomicFeatures_0.2.0.tar.gz' > Content type 'application/x-gzip' length 70108 bytes (68 Kb) > opened URL > ================================================== > downloaded 68 Kb > > trying URL 'http://www.bioconductor.org/packages/2.5/data/experiment /src/contrib/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.1.tar.gz' > Content type 'application/x-gzip' length 19774391 bytes (18.9 Mb) > opened URL > ================================================== > downloaded 18.9 Mb > > * installing *source* package ?RCurl? ... > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/cdu/library/RCurl? > * installing *source* package ?rtracklayer? ... > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > there is no package called 'RCurl' > Error : package 'RCurl' could not be loaded > ERROR: lazy loading failed for package ?rtracklayer? > * removing ?/home/cdu/library/rtracklayer? > * installing *source* package ?GenomicFeatures? ... > ** R > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > there is no package called 'rtracklayer' > Error : package 'rtracklayer' could not be loaded > ERROR: lazy loading failed for package ?GenomicFeatures? > * removing ?/home/cdu/library/GenomicFeatures? > * installing *source* package ?GenomicFeatures.Hsapiens.UCSC.hg18? ... > ** R > ** inst > ** preparing package for lazy loading > Error : package 'GenomicFeatures' required by 'GenomicFeatures.Hsapiens.UCSC.hg18' could not be found > ERROR: lazy loading failed for package ?GenomicFeatures.Hsapiens.UCSC.hg18? > * removing ?/home/cdu/library/GenomicFeatures.Hsapiens.UCSC.hg18? > > The downloaded packages are in > ?/tmp/Rtmp26fOPJ/downloaded_packages? > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'RCurl' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'rtracklayer' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'GenomicFeatures' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'GenomicFeatures.Hsapiens.UCSC.hg18' had non-zero exit status > > Can you help me with this? > > Thanks! > > > -- > Sincerely, > Changbin -- > > Changbin Du > DOE Joint Genome Institute > Bldg 400 Rm 457 > 2800 Mitchell Dr, Walnut Creet, CA 94598 > Phone: 925-927-2856 > Fax: 925-296-5850 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.4 years ago by Kasper Daniel Hansen6.4k
Answer: problem when try to install GenomicFeatures packages
0
gravatar for Chao-Jen Wong
9.4 years ago by
Chao-Jen Wong580
USA/Seattle/Fred Hutchinson Cancer Research Center
Chao-Jen Wong580 wrote:
Hi, Changbin, Are you using Linux or Mac OS? The reason that you cannot install the rtracklayer and GenomicFeatures packages is because the configuration for RCurl has failed. Either it couldn't find curl-config in your path or curl-config is not installed. On your X window, type "locate libcurl" to see if "libcurl.so" is present. If not, you will have to install curl-devel rpms (if you are using Linux) in order to install RCurl package. Chao-Jen Changbin Du wrote: > HI, Dear, > > I am a biginner of BIOconductor. When I try to install the > GenomicFeatures package, I failed two times. Here is the code in R > under Linux: > > > biocLite("GenomicFeatures.Hsapiens.UCSC.hg18") > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "GenomicFeatures.Hsapiens.UCSC.hg18" > Please wait... > > also installing the dependencies ?RCurl?, ?rtracklayer?, > ?GenomicFeatures? > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-1.tar.gz' > Content type 'application/x-gzip' length 800529 bytes (781 Kb) > opened URL > ================================================== > downloaded 781 Kb > > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/rtracklay er_1.6.0.tar.gz' > > Content type 'application/x-gzip' length 1363174 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GenomicFe atures_0.2.0.tar.gz' > > Content type 'application/x-gzip' length 70108 bytes (68 Kb) > opened URL > ================================================== > downloaded 68 Kb > > trying URL > 'http://www.bioconductor.org/packages/2.5/data/experiment/src/contri b/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.1.tar.gz' > > Content type 'application/x-gzip' length 19774391 bytes (18.9 Mb) > opened URL > ================================================== > downloaded 18.9 Mb > > * installing *source* package ?RCurl? ... > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/cdu/library/RCurl? > * installing *source* package ?rtracklayer? ... > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) : > there is no package called 'RCurl' > Error : package 'RCurl' could not be loaded > ERROR: lazy loading failed for package ?rtracklayer? > * removing ?/home/cdu/library/rtracklayer? > * installing *source* package ?GenomicFeatures? ... > ** R > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) : > there is no package called 'rtracklayer' > Error : package 'rtracklayer' could not be loaded > ERROR: lazy loading failed for package ?GenomicFeatures? > * removing ?/home/cdu/library/GenomicFeatures? > * installing *source* package ?GenomicFeatures.Hsapiens.UCSC.hg18? ... > ** R > ** inst > ** preparing package for lazy loading > Error : package 'GenomicFeatures' required by > 'GenomicFeatures.Hsapiens.UCSC.hg18' could not be found > ERROR: lazy loading failed for package > ?GenomicFeatures.Hsapiens.UCSC.hg18? > * removing ?/home/cdu/library/GenomicFeatures.Hsapiens.UCSC.hg18? > > The downloaded packages are in > ?/tmp/Rtmp26fOPJ/downloaded_packages? > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'RCurl' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'rtracklayer' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'GenomicFeatures' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'GenomicFeatures.Hsapiens.UCSC.hg18' had > non-zero exit status > > Can you help me with this? > > Thanks! > > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
ADD COMMENTlink written 9.4 years ago by Chao-Jen Wong580
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