problem updating packages OCPlus and RSNper
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@kimpel-mark-w-727
Last seen 8.4 years ago
I have recently migrated to R 2.4.0 and BioC 1.9 I cannot update packages OCPlus and RSNper from within R or from the web interface. Below are the errors I get and my sessionInfo() Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. OCplus : Version 1.7.0 installed in C:/PROGRA~1/R/R-24~1.0/library Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc Update (y/N/c)? y RSNPper : Version 1.6.3 installed in C:/PROGRA~1/R/R-24~1.0/library Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc Update (y/N/c)? y trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/cont rib/2.4/OCplus_1.8.0.zip' Error in download.file(url, destfile, method, mode = "wb") : cannot open URL 'http://bioconductor.org/packages/1.9/bioc/bin /windows/contrib/2.4/OCplus_1.8.0.zip' In addition: Warning messages: 1: Do not know which element of 'lib' to install dependencies into skipping dependencies in: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, 2: cannot open: HTTP status was '403 Forbidden' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'OCplus' failed trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/cont rib/2.4/RSNPper_1.8.0.zip' Error in download.file(url, destfile, method, mode = "wb") : cannot open URL 'http://bioconductor.org/packages/1.9/bioc/bin /windows/contrib/2.4/RSNPper_1.8.0.zip' In addition: Warning message: cannot open: HTTP status was '403 Forbidden' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'RSNPper' failed Loading required package: affy Loading required package: affyio [1] TRUE Loading required package: limma [1] TRUE > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" other attached packages: limma affy affyio Biobase "2.9.1" "1.12.0" "1.2.0" "1.12.0" >From the web interface (example is RSNper but get same message with OCPlus): http://www.bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/ RSNPper_1.8.0.zip Access forbidden! You don't have permission to access the requested object. It is either read-protected or not readable by the server. If you think this is a server error, please contact the webmaster. Error 403 www.bioconductor.org Mon Oct 9 08:46:36 2006 Apache/2.0.49 (Linux/SuSE) Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Work, & Mobile ? (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX
affy limma affyio OCplus affy limma affyio OCplus • 1.2k views
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@herve-pages-1542
Last seen 19 hours ago
Seattle, WA, United States
Hi Mark, There was a file permission issue on our server. It should be fixed now. Thanks for reporting this and sorry for the inconvenience! Best, H. Kimpel, Mark William wrote: > I have recently migrated to R 2.4.0 and BioC 1.9 I cannot update packages OCPlus and RSNper from within R or from the web interface. Below are the errors I get and my sessionInfo() > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > OCplus : > Version 1.7.0 installed in C:/PROGRA~1/R/R-24~1.0/library > Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc > Update (y/N/c)? y > RSNPper : > Version 1.6.3 installed in C:/PROGRA~1/R/R-24~1.0/library > Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc > Update (y/N/c)? y > trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/co ntrib/2.4/OCplus_1.8.0.zip' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL 'http://bioconductor.org/packages/1.9/bioc/b in/windows/contrib/2.4/OCplus_1.8.0.zip' > In addition: Warning messages: > 1: Do not know which element of 'lib' to install dependencies into > skipping dependencies in: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, > 2: cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package 'OCplus' failed > trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/co ntrib/2.4/RSNPper_1.8.0.zip' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL 'http://bioconductor.org/packages/1.9/bioc/b in/windows/contrib/2.4/RSNPper_1.8.0.zip' > In addition: Warning message: > cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package 'RSNPper' failed > Loading required package: affy > Loading required package: affyio > [1] TRUE > Loading required package: limma > [1] TRUE > >> sessionInfo() >> > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" > > other attached packages: > limma affy affyio Biobase > "2.9.1" "1.12.0" "1.2.0" "1.12.0" > > > >From the web interface (example is RSNper but get same message with OCPlus): > > http://www.bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2. 4/RSNPper_1.8.0.zip > > Access forbidden! > > You don't have permission to access the requested object. It is either read-protected or not readable by the server. > > If you think this is a server error, please contact the webmaster. > Error 403 > www.bioconductor.org > Mon Oct 9 08:46:36 2006 > Apache/2.0.49 (Linux/SuSE) > > Mark W. Kimpel MD > > > Official Business Address: > > Department of Psychiatry > Indiana University School of Medicine > PR M116 > Institute of Psychiatric Research > 791 Union Drive > Indianapolis, IN 46202 > > Preferred Mailing Address: > > 15032 Hunter Court > Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile > > (317) 663-0513 Home (no voice mail please) > 1-(317)-536-2730 FAX > > _______________________________________________ > 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 >
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Herve, Problem solved. Thanks! mark Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: Herve Pages [mailto:hpages@fhcrc.org] Sent: Monday, October 09, 2006 3:41 PM To: Kimpel, Mark William Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem updating packages OCPlus and RSNper Hi Mark, There was a file permission issue on our server. It should be fixed now. Thanks for reporting this and sorry for the inconvenience! Best, H. Kimpel, Mark William wrote: > I have recently migrated to R 2.4.0 and BioC 1.9 I cannot update packages OCPlus and RSNper from within R or from the web interface. Below are the errors I get and my sessionInfo() > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > OCplus : > Version 1.7.0 installed in C:/PROGRA~1/R/R-24~1.0/library > Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc > Update (y/N/c)? y > RSNPper : > Version 1.6.3 installed in C:/PROGRA~1/R/R-24~1.0/library > Version 1.8.0 available at http://bioconductor.org/packages/1.9/bioc > Update (y/N/c)? y > trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/OCp lu s_1.8.0.zip' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/OCp lu s_1.8.0.zip' > In addition: Warning messages: > 1: Do not know which element of 'lib' to install dependencies into > skipping dependencies in: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, > 2: cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package 'OCplus' failed > trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/RSN Pp er_1.8.0.zip' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/RSN Pp er_1.8.0.zip' > In addition: Warning message: > cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package 'RSNPper' failed > Loading required package: affy > Loading required package: affyio > [1] TRUE > Loading required package: limma > [1] TRUE > >> sessionInfo() >> > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" > > other attached packages: > limma affy affyio Biobase > "2.9.1" "1.12.0" "1.2.0" "1.12.0" > > > >From the web interface (example is RSNper but get same message with OCPlus): > > http://www.bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/ RS NPper_1.8.0.zip > > Access forbidden! > > You don't have permission to access the requested object. It is either read-protected or not readable by the server. > > If you think this is a server error, please contact the webmaster. > Error 403 > www.bioconductor.org > Mon Oct 9 08:46:36 2006 > Apache/2.0.49 (Linux/SuSE) > > Mark W. Kimpel MD > > > Official Business Address: > > Department of Psychiatry > Indiana University School of Medicine > PR M116 > Institute of Psychiatric Research > 791 Union Drive > Indianapolis, IN 46202 > > Preferred Mailing Address: > > 15032 Hunter Court > Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile > > (317) 663-0513 Home (no voice mail please) > 1-(317)-536-2730 FAX > > _______________________________________________ > 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 >
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