failed to install biocondoctuor

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wang peter ★ 2.0k

@wang-peter-4647

Last seen 10.3 years ago

i just reinstall the biocondoctuor in china. it is very slow, due to chinese restriction to foreign website and i meet such error, i never met before package annotate successfully unpacked and MD5 sums checked Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: packages base, boot, class, compiler, datasets, foreign, graphics, grDevices, grid, MASS, methods, nlme, parallel, spatial, splines, stats, stats4, tcltk, tools, utils are not available (for R version 2.15.2) 2: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 262334 != reported length 4200978 3: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 57623 != reported length 2346708 4: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 436576 != reported length 889011 5: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 1481998 != reported length 2048190 6: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 589241 != reported length 724724 7: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 123147 != reported length 3506196 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable reason 'No such file or directory' > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Chinese_People's Republic of China.936 [2] LC_CTYPE=Chinese_People's Republic of China.936 [3] LC_MONETARY=Chinese_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] tools_2.15.2 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.1 years ago by Dan Tenenbaum ★ 8.2k • written 11.1 years ago by wang peter ★ 2.0k

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Hi, On Tue, Dec 3, 2013 at 5:47 AM, Wang Peter <wng.peter at="" gmail.com=""> wrote: > i just reinstall the biocondoctuor in china. > it is very slow, due to chinese restriction to foreign website I never knew that was "a thing" ... seems rather unfortunate. Are there bioc (or at least CRAN) mirrors *within* China? Perhaps that might help. > and i meet such error, i never met before The errors below do seem rather strange. Seems to suggest that many files were only partially downloaded. I'd try another mirror first (even if you can't get one within China), and then I'd try to download the package (and its dependencies) that you are trying to install second to see if you can do it manually. I'd also suggest you upgrade to R 3.0.2 first before continuing. HTH, -steve > > > package ?annotate? successfully unpacked and MD5 sums checked > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) > : > cannot open the connection > In addition: Warning messages: > 1: packages ?base?, ?boot?, ?class?, ?compiler?, ?datasets?, ?foreign?, > ?graphics?, ?grDevices?, ?grid?, ?MASS?, ?methods?, ?nlme?, ?parallel?, > ?spatial?, ?splines?, ?stats?, ?stats4?, ?tcltk?, ?tools?, ?utils? are not > available (for R version 2.15.2) > 2: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 262334 != reported length 4200978 > 3: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 57623 != reported length 2346708 > 4: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 436576 != reported length 889011 > 5: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 1481998 != reported length 2048190 > 6: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 589241 != reported length 724724 > 7: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 123147 != reported length 3506196 > 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable reason > 'No such file or directory' >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=Chinese_People's Republic of China.936 > [2] LC_CTYPE=Chinese_People's Republic of China.936 > [3] LC_MONETARY=Chinese_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese_People's Republic of China.936 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] BiocInstaller_1.8.3 > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 -- Steve Lianoglou Computational Biologist Genentech

ADD COMMENT • link 11.1 years ago Steve Lianoglou ★ 13k

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 6 months ago

United States

You don't say which mirrors you are using. What is the output of: library(BiocInstaller) biocinstallRepos() ? Try using the mirror that Tengfei Yin set up in China: http://mirrors.ustc.edu.cn/bioc/ You should also pick a CRAN mirror in China, from this list: http://cran.r-project.org/mirrors.html Dan ----- Original Message ----- > From: "Wang Peter" <wng.peter at="" gmail.com=""> > To: bioconductor at r-project.org > Sent: Tuesday, December 3, 2013 5:47:32 AM > Subject: [BioC] failed to install biocondoctuor > > i just reinstall the biocondoctuor in china. > it is very slow, due to chinese restriction to foreign website > > and i meet such error, i never met before > > > package ?annotate? successfully unpacked and MD5 sums checked > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > "Type")) > : > cannot open the connection > In addition: Warning messages: > 1: packages ?base?, ?boot?, ?class?, ?compiler?, ?datasets?, > ?foreign?, > ?graphics?, ?grDevices?, ?grid?, ?MASS?, ?methods?, ?nlme?, > ?parallel?, > ?spatial?, ?splines?, ?stats?, ?stats4?, ?tcltk?, ?tools?, ?utils? > are not > available (for R version 2.15.2) > 2: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 262334 != reported length 4200978 > 3: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 57623 != reported length 2346708 > 4: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 436576 != reported length 889011 > 5: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 1481998 != reported length 2048190 > 6: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 589241 != reported length 724724 > 7: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 123147 != reported length 3506196 > 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip > file > 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > "Type")) : > cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable > reason > 'No such file or directory' > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=Chinese_People's Republic of China.936 > [2] LC_CTYPE=Chinese_People's Republic of China.936 > [3] LC_MONETARY=Chinese_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese_People's Republic of China.936 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] BiocInstaller_1.8.3 > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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

ADD COMMENT • link 11.1 years ago Dan Tenenbaum ★ 8.2k

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PS. An easy way to select mirrors is to use the functions chooseCRANmirror() and chooseBioCmirror() Dan ----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Wang Peter" <wng.peter at="" gmail.com=""> > Cc: bioconductor at r-project.org > Sent: Tuesday, December 3, 2013 8:32:26 AM > Subject: Re: [BioC] failed to install biocondoctuor > > You don't say which mirrors you are using. What is the output of: > > library(BiocInstaller) > biocinstallRepos() > > ? > > Try using the mirror that Tengfei Yin set up in China: > > http://mirrors.ustc.edu.cn/bioc/ > > You should also pick a CRAN mirror in China, from this list: > > http://cran.r-project.org/mirrors.html > > Dan > > > ----- Original Message ----- > > From: "Wang Peter" <wng.peter at="" gmail.com=""> > > To: bioconductor at r-project.org > > Sent: Tuesday, December 3, 2013 5:47:32 AM > > Subject: [BioC] failed to install biocondoctuor > > > > i just reinstall the biocondoctuor in china. > > it is very slow, due to chinese restriction to foreign website > > > > and i meet such error, i never met before > > > > > > package ?annotate? successfully unpacked and MD5 sums checked > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > > "Type")) > > : > > cannot open the connection > > In addition: Warning messages: > > 1: packages ?base?, ?boot?, ?class?, ?compiler?, ?datasets?, > > ?foreign?, > > ?graphics?, ?grDevices?, ?grid?, ?MASS?, ?methods?, ?nlme?, > > ?parallel?, > > ?spatial?, ?splines?, ?stats?, ?stats4?, ?tcltk?, ?tools?, ?utils? > > are not > > available (for R version 2.15.2) > > 2: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 262334 != reported length 4200978 > > 3: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 57623 != reported length 2346708 > > 4: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 436576 != reported length 889011 > > 5: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 1481998 != reported length 2048190 > > 6: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 589241 != reported length 724724 > > 7: In download.file(url, destfile, method, mode = "wb", ...) : > > downloaded length 123147 != reported length 3506196 > > 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip > > file > > 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > > "Type")) : > > cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable > > reason > > 'No such file or directory' > > > sessionInfo() > > R version 2.15.2 (2012-10-26) > > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > > [1] LC_COLLATE=Chinese_People's Republic of China.936 > > [2] LC_CTYPE=Chinese_People's Republic of China.936 > > [3] LC_MONETARY=Chinese_People's Republic of China.936 > > [4] LC_NUMERIC=C > > [5] LC_TIME=Chinese_People's Republic of China.936 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods > > base > > other attached packages: > > [1] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > > [1] tools_2.15.2 > > > > -- > > shan gao > > Room 231(Dr.Fei lab) > > Boyce Thompson Institute for Plant Research > > Cornell University > > Tower Road, Ithaca, NY 14853-1801 > > Office phone: 1-607-254-1267(day) > > Official email:sg839 at cornell.edu > > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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

ADD REPLY • link 11.1 years ago Dan Tenenbaum ★ 8.2k

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thank you very much On Wed, Dec 4, 2013 at 1:55 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > PS. An easy way to select mirrors is to use the functions > chooseCRANmirror() > and > chooseBioCmirror() > > Dan > > > ----- Original Message ----- > > From: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > To: "Wang Peter" <wng.peter@gmail.com> > > Cc: bioconductor@r-project.org > > Sent: Tuesday, December 3, 2013 8:32:26 AM > > Subject: Re: [BioC] failed to install biocondoctuor > > > > You don't say which mirrors you are using. What is the output of: > > > > library(BiocInstaller) > > biocinstallRepos() > > > > ? > > > > Try using the mirror that Tengfei Yin set up in China: > > > > http://mirrors.ustc.edu.cn/bioc/ > > > > You should also pick a CRAN mirror in China, from this list: > > > > http://cran.r-project.org/mirrors.html > > > > > > > Dan > > > > > > ----- Original Message ----- > > > From: "Wang Peter" <wng.peter@gmail.com> > > > To: bioconductor@r-project.org > > > Sent: Tuesday, December 3, 2013 5:47:32 AM > > > Subject: [BioC] failed to install biocondoctuor > > > > > > i just reinstall the biocondoctuor in china. > > > it is very slow, due to chinese restriction to foreign website > > > > > > and i meet such error, i never met before > > > > > > > > > package ï¿½annotateï¿½ successfully unpacked and MD5 sums checked > > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > > > "Type")) > > > : > > > cannot open the connection > > > In addition: Warning messages: > > > 1: packages ï¿½baseï¿½, ï¿½bootï¿½, ï¿½classï¿½, ï¿½compilerï¿½, ï¿½datasetsï¿½, > > > ï¿½foreignï¿½, > > > ï¿½graphicsï¿½, ï¿½grDevicesï¿½, ï¿½gridï¿½, ï¿½MASSï¿½, ï¿½methodsï¿½, ï¿½nlmeï¿½, > > > ï¿½parallelï¿½, > > > ï¿½spatialï¿½, ï¿½splinesï¿½, ï¿½statsï¿½, ï¿½stats4ï¿½, ï¿½tcltkï¿½, ï¿½toolsï¿½, ï¿½utilsï¿½ > > > are not > > > available (for R version 2.15.2) > > > 2: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 262334 != reported length 4200978 > > > 3: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 57623 != reported length 2346708 > > > 4: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 436576 != reported length 889011 > > > 5: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 1481998 != reported length 2048190 > > > 6: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 589241 != reported length 724724 > > > 7: In download.file(url, destfile, method, mode = "wb", ...) : > > > downloaded length 123147 != reported length 3506196 > > > 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip > > > file > > > 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", > > > "Type")) : > > > cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable > > > reason > > > 'No such file or directory' > > > > sessionInfo() > > > R version 2.15.2 (2012-10-26) > > > Platform: i386-w64-mingw32/i386 (32-bit) > > > locale: > > > [1] LC_COLLATE=Chinese_People's Republic of China.936 > > > [2] LC_CTYPE=Chinese_People's Republic of China.936 > > > [3] LC_MONETARY=Chinese_People's Republic of China.936 > > > [4] LC_NUMERIC=C > > > [5] LC_TIME=Chinese_People's Republic of China.936 > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods > > > base > > > other attached packages: > > > [1] BiocInstaller_1.8.3 > > > loaded via a namespace (and not attached): > > > [1] tools_2.15.2 > > > > > > -- > > > shan gao > > > Room 231(Dr.Fei lab) > > > Boyce Thompson Institute for Plant Research > > > Cornell University > > > Tower Road, Ithaca, NY 14853-1801 > > > Office phone: 1-607-254-1267(day) > > > Official email:sg839@cornell.edu > > > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > > > > > [[alternative HTML version deleted]] > > > > > > > > > _______________________________________________ > > > 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 > > > > _______________________________________________ > > 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 > -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

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