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Question: fatal error when installint BioC devel on R devel
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gravatar for Martin Rijlaarsdam
3.7 years ago by
Martin Rijlaarsdam190 wrote:
Dear Sirs, When trying to install the devel version of Bioconductor on a clean install of R devel I got the following errors: *source("http://bioconductor.org/biocLite.R <http: bioconductor.org="" bioclite.r="">")* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 <http: www.bioconductor.org="" packages="" 2.14="" bioc="" bin="" windows="" contrib="" 3.="" 2="">* * package 'BiocInstaller' is available as a source package but not as a binary* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller",* * repos="http://www.bioconductor.org/packages/2.14/bioc <http: www.bioconductor.org="" packages="" 2.14="" bioc="">")'* Next, I tried: *install.packages("BiocInstaller",repos="http://www.bioconductor.org/p ackages/2.14/bioc <http: www.bioconductor.org="" packages="" 2.14="" bioc="">", type="source")* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstal ler_1.13.3.tar.gz <http: www.bioconductor.org="" packages="" 2.14="" bioc="" src="" contrib="" biocinstal="" ler_1.13.3.tar.gz="">'* *Content type 'application/x-gzip' length 14183 bytes (13 Kb)* *opened URL* *downloaded 13 Kb* ** installing *source* package 'BiocInstaller' ...* *** R* *** inst* *** preparing package for lazy loading* *** help* **** installing help indices* *** building package indices* *** testing if installed package can be loaded* **** arch - i386* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* **** arch - x64* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* ** DONE (BiocInstaller)* *The downloaded source packages are in* * 'C:\Users\lepo\AppData\Local\Temp\RtmpoRLBWv\downloaded_packages'* I then tried to install the default packages and the Gviz package: *source("http://bioconductor.org/biocLite.R <http: bioconductor.org="" bioclite.r="">")* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* *biocLite()* *Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/2.14/bioc <http: bioconductor.org="" packages="" 2.14="" bioc="">* *biocLite("Gviz")* *Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/2.14/bioc <http: bioconductor.org="" packages="" 2.14="" bioc="">* Am I doing something fundamentally wrong here? Or is it a Bioconductor issue? I am using Windows 7 64 bits and have no firewall enabled. Several other (non-devel) versions of R and Bioconductor work find on this machine. The problem occurs in both the 64bits and 32bits version of R devel. Thanks for any help! Best wishes, Martin *sessionInfo()* *R Under development (unstable) (2014-03-12 r65176)* *Platform: x86_64-w64-mingw32/x64 (64-bit)* *locale:* *[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252* *[4] LC_NUMERIC=C LC_TIME=English_United States.1252 * *attached base packages:* *[1] stats graphics grDevices utils datasets methods base * *other attached packages:* *[1] BiocInstaller_1.13.3* *loaded via a namespace (and not attached):* *[1] tools_3.2.0* -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Martin Rijlaarsdam190
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gravatar for Martin Rijlaarsdam
3.7 years ago by
Martin Rijlaarsdam190 wrote:
Dear list, My apologies, this should have been posted to the BioC devel list. Please ignore this post here. Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Thu, Mar 13, 2014 at 9:46 AM, Martin Rijlaarsdam < m.a.rijlaarsdam@gmail.com> wrote: > Dear Sirs, > > When trying to install the devel version of Bioconductor on a clean > install of R devel I got the following errors: > > *source("http://bioconductor.org/biocLite.R > <http: bioconductor.org="" bioclite.r="">")* > *Warning in install.packages :* > * package 'BiocInstaller' is not available (for R Under development)* > *Installing package into 'C:/Users/lepo/Documents/R/win- library/3.2'* > *(as 'lib' is unspecified)* > *Warning in install.packages :* > * cannot open: HTTP status was '404 Not Found'* > *Warning in install.packages :* > * cannot open: HTTP status was '404 Not Found'* > *Warning in install.packages :* > * unable to access index for repository > http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 > <http: www.bioconductor.org="" packages="" 2.14="" bioc="" bin="" windows="" contrib="" 3.2="">* > > * package 'BiocInstaller' is available as a source package but not as a > binary* > > *Warning in install.packages :* > * package 'BiocInstaller' is not available (for R Under development)* > *'biocLite.R' failed to install 'BiocInstaller', use > 'install.packages("BiocInstaller",* > * repos="http://www.bioconductor.org/packages/2.14/bioc > <http: www.bioconductor.org="" packages="" 2.14="" bioc="">")'* > > Next, I tried: > *install.packages("BiocInstaller",repos="http://www.bioconductor.org /packages/2.14/bioc > <http: www.bioconductor.org="" packages="" 2.14="" bioc="">", type="source")* > *Installing package into 'C:/Users/lepo/Documents/R/win- library/3.2'* > *(as 'lib' is unspecified)* > *trying URL > 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInst aller_1.13.3.tar.gz > <http: www.bioconductor.org="" packages="" 2.14="" bioc="" src="" contrib="" biocinst="" aller_1.13.3.tar.gz="">'* > *Content type 'application/x-gzip' length 14183 bytes (13 Kb)* > *opened URL* > *downloaded 13 Kb* > > ** installing *source* package 'BiocInstaller' ...* > *** R* > *** inst* > *** preparing package for lazy loading* > *** help* > **** installing help indices* > *** building package indices* > *** testing if installed package can be loaded* > **** arch - i386* > *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* > **** arch - x64* > *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* > ** DONE (BiocInstaller)* > > *The downloaded source packages are in* > * 'C:\Users\lepo\AppData\Local\Temp\RtmpoRLBWv\downloaded_packages'* > > I then tried to install the default packages and the Gviz package: > > *source("http://bioconductor.org/biocLite.R > <http: bioconductor.org="" bioclite.r="">")* > *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* > > *biocLite()* > *Error: 'no packages in repository (no internet connection?)' while trying > http://bioconductor.org/packages/2.14/bioc > <http: bioconductor.org="" packages="" 2.14="" bioc="">* > > *biocLite("Gviz")* > *Error: 'no packages in repository (no internet connection?)' while trying > http://bioconductor.org/packages/2.14/bioc > <http: bioconductor.org="" packages="" 2.14="" bioc="">* > > Am I doing something fundamentally wrong here? Or is it a Bioconductor > issue? > > I am using Windows 7 64 bits and have no firewall enabled. Several other > (non-devel) versions of R and Bioconductor work find on this machine. The > problem occurs in both the 64bits and 32bits version of R devel. > > Thanks for any help! > > Best wishes, > Martin > > *sessionInfo()* > *R Under development (unstable) (2014-03-12 r65176)* > *Platform: x86_64-w64-mingw32/x64 (64-bit)* > > *locale:* > *[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252* > *[4] LC_NUMERIC=C LC_TIME=English_United > States.1252 * > > *attached base packages:* > *[1] stats graphics grDevices utils datasets methods base * > > *other attached packages:* > *[1] BiocInstaller_1.13.3* > > *loaded via a namespace (and not attached):* > *[1] tools_3.2.0* > > -- > M.A. (Martin) Rijlaarsdam MSc. MD > Erasmus MC - University Medical Center Rotterdam > Department of Pathology > Room Be-432b > Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > Email: m.a.rijlaarsdam@gmail.com > Mobile: +31 6 45408508 > Telephone (work): +31 10 7033409 > Fax +31 10 7044365 > Website: http://www.martinrijlaarsdam.nl > [[alternative HTML version deleted]]
ADD COMMENTlink written 3.7 years ago by Martin Rijlaarsdam190
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