getBioC and install.packages2 fail
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@arnemullersanofi-aventiscom-1086
Last seen 8.1 years ago
Hello, I've an installation problem. I'm running R 2.0.1 and BioC 1.5. . I'd like to install the 'proteomics' package. Getting the most recent getBioC fucntion works fine (I'm behind a firewall). ReposTools and tools get loaded automatically and then the script terminates without any error message and withour installing the proteomics package: > getBioC(libNam='proteomics', method='wget') Running getBioC version 1.2.69.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Loading required package: reposTools Loading required package: tools When running install.packages2('gpls') nothing happens either, no error, no output no instllation :-( Any ideas what goes wrong? thanks a lot for your help, Arne
Proteomics reposTools Proteomics reposTools • 881 views
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@adaikalavan-ramasamy-675
Last seen 8.1 years ago
What OS ? Are you able to do this successfully ? download.file( "http://www.bioconductor.org/repository/release1.5/package/Source/gpls _1.0.6.tar.gz", destfile="/tmp/junk" ) If yes, that should rule out any firewall problem. If no, then see help (download.file) or search the R-help archives for solution. If you are able to download successfully,then it might be some problem with installation. Since proteomics comprises only 3 packages, it might be worth to just download them manually and install it. Regards, Adai On Tue, 2005-03-29 at 17:00 +0200, Arne.Muller@sanofi-aventis.com wrote: > Hello, > > I've an installation problem. I'm running R 2.0.1 and BioC 1.5. . I'd like to install the 'proteomics' package. Getting the most recent getBioC fucntion works fine (I'm behind a firewall). ReposTools and tools get loaded automatically and then the script terminates without any error message and withour installing the proteomics package: > > > getBioC(libNam='proteomics', method='wget') > Running getBioC version 1.2.69.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > Loading required package: reposTools > Loading required package: tools > > When running install.packages2('gpls') > > nothing happens either, no error, no output no instllation :-( > > Any ideas what goes wrong? > > thanks a lot for your help, > > Arne > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
Hi Arne, <arne.muller@sanofi-aventis.com> writes: > I've an installation problem. I'm running R 2.0.1 and BioC > 1.5. . I'd like to install the 'proteomics' package. Getting the > most recent getBioC fucntion works fine (I'm behind a > firewall). ReposTools and tools get loaded automatically and then > the script terminates without any error message and withour > installing the proteomics package: > >> getBioC(libNam='proteomics', method='wget') > Running getBioC version 1.2.69.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > Loading required package: reposTools > Loading required package: tools > > When running install.packages2('gpls') > > nothing happens either, no error, no output no instllation :-( Hmm. On Linux with R 2.0.1 I'm able to install the proteomics package. You wrote that you are behind a firewall. Do you also have a web proxy? What happens if you do install.packages2("gpls") from the R prompt? + seth
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@arnemullersanofi-aventiscom-1086
Last seen 8.1 years ago
Thanks for your reply. I forgot to mentione the OS (linux RH 7.3), wget 1.8.1 and reposTools 1.5.2. I'm behind a firewall that requires authentification (it's a web-procy, too), but the code below (download.file) works, so I guess it's a problem with the existing installation. Well, or maybe it is a proxy probelm? regards, Arne ps: install.packages2("gpls") from the R prompt does not work either :-( > -----Original Message----- > From: Adaikalavan Ramasamy [mailto:ramasamy@cancer.org.uk] > Sent: 29 March 2005 17:28 > To: Muller, Arne PH/FR > Cc: BioConductor mailing list > Subject: Re: [BioC] getBioC and install.packages2 fail > > > What OS ? Are you able to do this successfully ? > > download.file( > "http://www.bioconductor.org/repository/release1.5/package/Sou > rce/gpls_1.0.6.tar.gz", destfile="/tmp/junk" ) > > If yes, that should rule out any firewall problem. If no, > then see help > (download.file) or search the R-help archives for solution. > > If you are able to download successfully,then it might be some problem > with installation. > > Since proteomics comprises only 3 packages, it might be worth to just > download them manually and install it. > > Regards, Adai > > > > On Tue, 2005-03-29 at 17:00 +0200, > Arne.Muller@sanofi-aventis.com wrote: > > Hello, > > > > I've an installation problem. I'm running R 2.0.1 and BioC > 1.5. . I'd like to install the 'proteomics' package. Getting > the most recent getBioC fucntion works fine (I'm behind a > firewall). ReposTools and tools get loaded automatically and > then the script terminates without any error message and > withour installing the proteomics package: > > > > > getBioC(libNam='proteomics', method='wget') > > Running getBioC version 1.2.69.... > > If you encounter problems, first make sure that > > you are running the latest version of getBioC() > > which can be found at: www.bioconductor.org/getBioC.R > > > > Please direct any concerns or questions to > bioconductor@stat.math.ethz.ch. > > > > Loading required package: reposTools > > Loading required package: tools > > > > When running install.packages2('gpls') > > > > nothing happens either, no error, no output no instllation :-( > > > > Any ideas what goes wrong? > > > > thanks a lot for your help, > > > > Arne > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
<arne.muller@sanofi-aventis.com> writes: > I forgot to mentione the OS (linux RH 7.3), wget 1.8.1 and > reposTools 1.5.2. I'm behind a firewall that requires > authentification (it's a web-procy, too), but the code below > (download.file) works, so I guess it's a problem with the existing > installation. Well, or maybe it is a proxy probelm? I suspect that it is a proxy problem. > ps: install.packages2("gpls") from the R prompt does not work either > :-( And by "does not work", you mean it hangs? Prints an error message? Help me out here. In your original post, you wanted to install the proteomics related packages: gpls, PROcess, and apComplex. apComplex is missing from the release1.5 repository and I'm looking into why. The other two are present. If gpls and PROcess would be of use to you, please try the following: >From an R session enter: biocUrl <- "http://www.bioconductor.org/packages/bioc/stable" install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl, dependencies=TRUE, method="wget") And let us know if it works (and if not, send us the error output ;-) + seth > >> -----Original Message----- >> From: Adaikalavan Ramasamy [mailto:ramasamy@cancer.org.uk] >> Sent: 29 March 2005 17:28 >> To: Muller, Arne PH/FR >> Cc: BioConductor mailing list >> Subject: Re: [BioC] getBioC and install.packages2 fail >> >> >> What OS ? Are you able to do this successfully ? >> >> download.file( >> "http://www.bioconductor.org/repository/release1.5/package/Sou >> rce/gpls_1.0.6.tar.gz", destfile="/tmp/junk" ) >> >> If yes, that should rule out any firewall problem. If no, >> then see help >> (download.file) or search the R-help archives for solution. >> >> If you are able to download successfully,then it might be some problem >> with installation. >> >> Since proteomics comprises only 3 packages, it might be worth to just >> download them manually and install it. >> >> Regards, Adai >> >> >> >> On Tue, 2005-03-29 at 17:00 +0200, >> Arne.Muller@sanofi-aventis.com wrote: >> > Hello, >> > >> > I've an installation problem. I'm running R 2.0.1 and BioC >> 1.5. . I'd like to install the 'proteomics' package. Getting >> the most recent getBioC fucntion works fine (I'm behind a >> firewall). ReposTools and tools get loaded automatically and >> then the script terminates without any error message and >> withour installing the proteomics package: >> > >> > > getBioC(libNam='proteomics', method='wget') >> > Running getBioC version 1.2.69.... >> > If you encounter problems, first make sure that >> > you are running the latest version of getBioC() >> > which can be found at: www.bioconductor.org/getBioC.R >> > >> > Please direct any concerns or questions to >> bioconductor@stat.math.ethz.ch. >> > >> > Loading required package: reposTools >> > Loading required package: tools >> > >> > When running install.packages2('gpls') >> > >> > nothing happens either, no error, no output no instllation :-( >> > >> > Any ideas what goes wrong? >> > >> > thanks a lot for your help, >> > >> > Arne >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >> >>
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@arnemullersanofi-aventiscom-1086
Last seen 8.1 years ago
Thanks, When doing getBioC(libName='proteomics') I don't get any error message at all: > getBioC(libNam='proteomics', method='wget') Running getBioC version 1.2.69.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Loading required package: reposTools Loading required package: tools > The "install.packages" command prints an error, for some reason the proxy authentification failed! > install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl,dependencies=TRUE, me thod="wget") --12:07:56-- http://www.bioconductor.org/packages/bioc/stable/src/contrib/PACKA GES => `/tmp/RtmpEi1pKG/file74b0dc51' Resolving firewall... done. Connecting to firewall[XXX.XXX.XXX.XXX]:XX... connected. Proxy request sent, awaiting response... 407 Proxy Authentication Required 12:07:56 ERROR 407: Proxy Authentication Required. dependencies 'gpls''PROcess' are not available Warning message: Download had nonzero exit status in: download.file(url = paste(contriburl, "PACK AGES", sep = "/"), > However, when I connect to the web via mozilla (linux RH 7.3) and *then* run the install.packages the packages get downaloaded and installed properly. I guess this means there's something wrong with my proxy authentification. By the way, when running > source("http://www.bioconductor.org/getBioC.R") > getBioC(libName='proteomics') under w2k (using R --internet2) the installation works straight away ... Another hint that my proxy authentification under linux may be screwed up. kind regards, Arne > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of > Seth Falcon > Sent: 29 March 2005 19:57 > To: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] getBioC and install.packages2 fail > > > <arne.muller@sanofi-aventis.com> writes: > > I forgot to mentione the OS (linux RH 7.3), wget 1.8.1 and > > reposTools 1.5.2. I'm behind a firewall that requires > > authentification (it's a web-procy, too), but the code below > > (download.file) works, so I guess it's a problem with the existing > > installation. Well, or maybe it is a proxy probelm? > > I suspect that it is a proxy problem. > > > ps: install.packages2("gpls") from the R prompt does not work either > > :-( > > And by "does not work", you mean it hangs? Prints an error message? > Help me out here. > > In your original post, you wanted to install the proteomics related > packages: gpls, PROcess, and apComplex. > > apComplex is missing from the release1.5 repository and I'm looking > into why. The other two are present. > > If gpls and PROcess would be of use to you, please try the following: > > >From an R session enter: > > biocUrl <- "http://www.bioconductor.org/packages/bioc/stable" > install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl, > dependencies=TRUE, method="wget") > > And let us know if it works (and if not, send us the error output ;-) > > + seth > > > > > > > > > >> -----Original Message----- > >> From: Adaikalavan Ramasamy [mailto:ramasamy@cancer.org.uk] > >> Sent: 29 March 2005 17:28 > >> To: Muller, Arne PH/FR > >> Cc: BioConductor mailing list > >> Subject: Re: [BioC] getBioC and install.packages2 fail > >> > >> > >> What OS ? Are you able to do this successfully ? > >> > >> download.file( > >> "http://www.bioconductor.org/repository/release1.5/package/Sou > >> rce/gpls_1.0.6.tar.gz", destfile="/tmp/junk" ) > >> > >> If yes, that should rule out any firewall problem. If no, > >> then see help > >> (download.file) or search the R-help archives for solution. > >> > >> If you are able to download successfully,then it might be > some problem > >> with installation. > >> > >> Since proteomics comprises only 3 packages, it might be > worth to just > >> download them manually and install it. > >> > >> Regards, Adai > >> > >> > >> > >> On Tue, 2005-03-29 at 17:00 +0200, > >> Arne.Muller@sanofi-aventis.com wrote: > >> > Hello, > >> > > >> > I've an installation problem. I'm running R 2.0.1 and BioC > >> 1.5. . I'd like to install the 'proteomics' package. Getting > >> the most recent getBioC fucntion works fine (I'm behind a > >> firewall). ReposTools and tools get loaded automatically and > >> then the script terminates without any error message and > >> withour installing the proteomics package: > >> > > >> > > getBioC(libNam='proteomics', method='wget') > >> > Running getBioC version 1.2.69.... > >> > If you encounter problems, first make sure that > >> > you are running the latest version of getBioC() > >> > which can be found at: www.bioconductor.org/getBioC.R > >> > > >> > Please direct any concerns or questions to > >> bioconductor@stat.math.ethz.ch. > >> > > >> > Loading required package: reposTools > >> > Loading required package: tools > >> > > >> > When running install.packages2('gpls') > >> > > >> > nothing happens either, no error, no output no instllation :-( > >> > > >> > Any ideas what goes wrong? > >> > > >> > thanks a lot for your help, > >> > > >> > Arne > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@stat.math.ethz.ch > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > > >> > >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
<arne.muller@sanofi-aventis.com> writes: > The "install.packages" command prints an error, for some reason the proxy authentification failed! > >> install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl,dependencies=TRUE, me > thod="wget") > --12:07:56-- http://www.bioconductor.org/packages/bioc/stable/src/contrib/PACKA > GES > => `/tmp/RtmpEi1pKG/file74b0dc51' > Resolving firewall... done. > Connecting to firewall[XXX.XXX.XXX.XXX]:XX... connected. > Proxy request sent, awaiting response... 407 Proxy Authentication Required > 12:07:56 ERROR 407: Proxy Authentication Required. This output is from wget and indicates the proxy auth problem you suspect. Perhaps rereading the help in download.file and/or interacting with a local sysadmin will help. Best, + seth
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Arne, Seth is very likely to be correct. Reading help("download.file") shows that the default method is "internal" and it appears that your internal method does not care about proxies etc. In the details section of help("download.file"), you will find Method '"wget"' can be used with proxy firewalls which require user/password authentication if proper values are stored in the configuration file for 'wget'. and to setup the configuration file for 'wget' see the "Setting Proxies" section under the same help file. Was there a specific reason for using the argument method="wget" in getBioC() ? Regards, Adai On Wed, 2005-03-30 at 06:57 -0800, Seth Falcon wrote: > <arne.muller@sanofi-aventis.com> writes: > > The "install.packages" command prints an error, for some reason the proxy authentification failed! > > > >> install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl,dependencies=TRUE, me > > thod="wget") > > --12:07:56-- http://www.bioconductor.org/packages/bioc/stable/src/contrib/PACKA > > GES > > => `/tmp/RtmpEi1pKG/file74b0dc51' > > Resolving firewall... done. > > Connecting to firewall[XXX.XXX.XXX.XXX]:XX... connected. > > Proxy request sent, awaiting response... 407 Proxy Authentication Required > > 12:07:56 ERROR 407: Proxy Authentication Required. > > This output is from wget and indicates the proxy auth problem you > suspect. Perhaps rereading the help in download.file and/or > interacting with a local sysadmin will help. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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