An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20080904/024cfa5d/attachment.pl>
Error with update.packages()
3 messages · Brian Ripley, Brant Inman
Try another mirror: this is not the first time we've seen problems at www.ibiblio.org.
On Thu, 4 Sep 2008, Brant Inman wrote:
R-helpers: I just updated from R 7.0 to R 7.2.2 today. I am using MAC OS X version 10.5.4 on a Macbook to run R. ----------------------------
sessionInfo()
R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.2 ---------------------------- When I tried to update my packages, I got the following messages: ----------------------------
update.packages()
Amelia : Version 1.1-30 installed in /Library/Frameworks/R.framework/ Resources/library Version 1.1-33 available at http://www.ibiblio.org/pub/languages/R/ CRAN Update (y/N/c)? y empiricalBayes : Version 2.0 installed in /Library/Frameworks/R.framework/Resources/ library Version 2.1 available at http://www.ibiblio.org/pub/languages/R/CRAN Update (y/N/c)? y Matrix : Version 0.999375-9 installed in /Library/Frameworks/R.framework/ Resources/library Version 0.999375-11 available at http://www.ibiblio.org/pub/languages/R/CRAN Update (y/N/c)? y ...<snip, all seems well>.... also installing the dependencies ?sandwich?, ?strucchange?, ?vcd?, ?rrcov?, ?spam? trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/sandwich_2.1-0.tgz' Content type 'application/x-gzip' length 678518 bytes (662 Kb) opened URL ================================================== downloaded 662 Kb trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/strucchange_1.3-3.tgz' Content type 'application/x-gzip' length 777150 bytes (758 Kb) opened URL ================================================== downloaded 758 Kb ...<snip, the errors begin>.... trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/rrcov_0.4-06.tgz' Content type 'application/x-gzip' length 365965 bytes (357 Kb) opened URL ========================================== downloaded 304 Kb trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz' In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 312279 != reported length 365965 2: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'spam' failed trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'Amelia' failed ...<snip, the errors continue>.... In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'zoo' failed gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default ---------------------------- The first part of the procedure seemed to work, then came page after page of error messages. Can someone tell me what is going on here and how I can fix the problem? I found a similar report on R-help that was never resolved and also involved a MAC (http://tolstoy.newcastle.edu.au/R/e4/help/08/06/15556.html ). Could this be a MAC issue? Thanks very much for your time. Brant Inman [[alternative HTML version deleted]]
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Thank you for your suggestion. I did as you suggested and switched from USA (NC) to USA (IA). Again, the packages seemed to download OK but this time a single error message appeared: ---------- ...<snip>... ================================================== downloaded 168 Kb trying URL 'http://streaming.stat.iastate.edu/CRAN/bin/macosx/universal/contrib/2.7/zoo_1.5-4.tgz' Content type 'application/x-gzip' length 749912 bytes (732 Kb) opened URL ================================================== downloaded 732 Kb Error: cannot remove prior installation of package ?fSeries? > ---------- This error appears to have stopped the package updating, since when I type update.packages() again, the whole list of packages is generated, implying that they have not been updated. Any other suggestions? Would uninstalling R and then reinstalling it help? Brant ---------
On Sep 4, 2008, at 2:59 PM, Prof Brian Ripley wrote:
Try another mirror: this is not the first time we've seen problems at www.ibiblio.org. On Thu, 4 Sep 2008, Brant Inman wrote:
R-helpers: I just updated from R 7.0 to R 7.2.2 today. I am using MAC OS X version 10.5.4 on a Macbook to run R. ----------------------------
sessionInfo()
R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.2 ---------------------------- When I tried to update my packages, I got the following messages: ----------------------------
update.packages()
Amelia : Version 1.1-30 installed in /Library/Frameworks/R.framework/ Resources/library Version 1.1-33 available at http://www.ibiblio.org/pub/languages/R/ CRAN Update (y/N/c)? y empiricalBayes : Version 2.0 installed in /Library/Frameworks/R.framework/Resources/ library Version 2.1 available at http://www.ibiblio.org/pub/languages/R/CRAN Update (y/N/c)? y Matrix : Version 0.999375-9 installed in /Library/Frameworks/R.framework/ Resources/library Version 0.999375-11 available at http://www.ibiblio.org/pub/languages/R/CRAN Update (y/N/c)? y ...<snip, all seems well>.... also installing the dependencies ?sandwich?, ?strucchange?, ?vcd?, ?rrcov?, ?spam? trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/sandwich_2.1-0.tgz' Content type 'application/x-gzip' length 678518 bytes (662 Kb) opened URL ================================================== downloaded 662 Kb trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/strucchange_1.3-3.tgz' Content type 'application/x-gzip' length 777150 bytes (758 Kb) opened URL ================================================== downloaded 758 Kb ...<snip, the errors begin>.... trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/rrcov_0.4-06.tgz' Content type 'application/x-gzip' length 365965 bytes (357 Kb) opened URL ========================================== downloaded 304 Kb trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz' In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 312279 != reported length 365965 2: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'spam' failed trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'Amelia' failed ...<snip, the errors continue>.... In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : unable to connect to 'mirrors.ibiblio.org' on port 80. Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'zoo' failed gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default ---------------------------- The first part of the procedure seemed to work, then came page after page of error messages. Can someone tell me what is going on here and how I can fix the problem? I found a similar report on R-help that was never resolved and also involved a MAC (http://tolstoy.newcastle.edu.au/R/e4/help/08/06/15556.html ). Could this be a MAC issue? Thanks very much for your time. Brant Inman [[alternative HTML version deleted]]
-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595