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Question: problem installing XML
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4.7 years ago by
Guest User12k
Guest User12k wrote:
Dear BioC, I am having some difficulty installing XML. Please see below for error message and session info.. Best regards, Anthony > setInternet2(TRUE) > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite("XML") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'XML' trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' Content type 'application/zip' length 4288136 bytes (4.1 Mb) opened URL downloaded 4.1 Mb Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 4259840 != reported length 4288136 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file or directory' -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.7 years ago by Anthony Bosco20 • written 4.7 years ago by Guest User12k
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gravatar for James W. MacDonald
4.7 years ago by
United States
James W. MacDonald48k wrote:
Hi Anthony, Looks like you got a corrupted download. I just tried this and it worked without problems. Have you tried again? > biocLite("XML") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'XML' trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' Content type 'application/zip' length 4288136 bytes (4.1 Mb) opened URL downloaded 4.1 Mb package ?XML? successfully unpacked and MD5 sums checked > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] tools_3.0.2 Best, Jim On 3/26/2014 12:44 AM, Anthony Bosco [guest] wrote: > Dear BioC, > > I am having some difficulty installing XML. > > Please see below for error message and session info.. > > Best regards, > > Anthony > >> setInternet2(TRUE) >> source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> biocLite("XML") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > Installing package(s) 'XML' > trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' > Content type 'application/zip' length 4288136 bytes (4.1 Mb) > opened URL > downloaded 4.1 Mb > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open the connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 4259840 != reported length 4288136 > 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file or directory' > > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.7 years ago by James W. MacDonald48k
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gravatar for Anthony Bosco
4.7 years ago by
Anthony Bosco20 wrote:
Hi James, Its working fine now.. Thanks very much.. Best regards, Anthony -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Wed 3/26/2014 9:30 PM To: Anthony Bosco [guest] Cc: bioconductor@r-project.org; Anthony Bosco Subject: Re: [BioC] problem installing XML Hi Anthony, Looks like you got a corrupted download. I just tried this and it worked without problems. Have you tried again? > biocLite("XML") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'XML' trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' Content type 'application/zip' length 4288136 bytes (4.1 Mb) opened URL downloaded 4.1 Mb package 'XML' successfully unpacked and MD5 sums checked > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] tools_3.0.2 Best, Jim On 3/26/2014 12:44 AM, Anthony Bosco [guest] wrote: > Dear BioC, > > I am having some difficulty installing XML. > > Please see below for error message and session info.. > > Best regards, > > Anthony > >> setInternet2(TRUE) >> source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> biocLite("XML") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > Installing package(s) 'XML' > trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' > Content type 'application/zip' length 4288136 bytes (4.1 Mb) > opened URL > downloaded 4.1 Mb > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open the connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 4259840 != reported length 4288136 > 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file or directory' > > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]
ADD COMMENTlink written 4.7 years ago by Anthony Bosco20
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