Bioconductor on Unix: cannot load the library affy
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@duhaime-johanne-162
Last seen 10.2 years ago
Hello I have installed R (1.7.0) and Bionconductor (1.1) on Unix (Solaris 2.6). I had no problem for the installation. When I want to load the package affy (library(affy)) I have an error message as shown below. Here are the error, the ~Renviron file and the libraries installed. ---------------------------------------------------------------------- --------------------------------------------------------------------- mercure{sasircm}103: bin/R R : Copyright 2003, The R Development Core Team Version 1.7.0 (2003-04-16) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type `license()' or `licence()' for distribution details. R is a collaborative project with many contributors. Type `contributors()' for more information. Type `demo()' for some demos, `help()' for on-line help, or `help.start()' for a HTML browser interface to help. Type `q()' to quit R. > library(affy) Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : This is not a valid package -- no DESCRIPTION exists Error in library(affy) : .First.lib failed > q() Save workspace image? [y/n/c]: n mercure{sasircm}104: more ~/.Renviron R_LIBS="/opt/sasircm/R/R-1.7.0/lib" mercure{sasircm}105: l /opt/sasircm/R/R-1.7.0/lib total 38 drwxrwxrwx 18 sasircm sequence 512 May 8 14:56 ./ drwxrwxrwx 16 sasircm sequence 1024 May 8 14:42 ../ drwxr-xr-x 12 sasircm sequence 512 May 8 14:45 Biobase/ -rw-r--r-- 1 sasircm sequence 608 May 8 14:56 R.css drwxr-xr-x 10 sasircm sequence 512 May 8 14:45 ROC/ drwxr-xr-x 14 sasircm sequence 512 May 8 14:56 affy/ drwxr-xr-x 12 sasircm sequence 512 May 8 14:45 annotate/ drwxr-xr-x 10 sasircm sequence 512 May 8 14:45 edd/ drwxr-xr-x 12 sasircm sequence 512 May 8 14:45 genefilter/ drwxr-xr-x 10 sasircm sequence 512 May 8 14:45 geneplotter/ drwxr-xr-x 11 sasircm sequence 512 May 8 14:48 graph/ drwxr-xr-x 11 sasircm sequence 512 May 8 14:48 hexbin/ drwxr-xr-x 10 sasircm sequence 512 May 8 14:46 marrayClasses/ drwxr-xr-x 11 sasircm sequence 512 May 8 14:46 marrayInput/ drwxr-xr-x 10 sasircm sequence 512 May 8 14:47 marrayNorm/ drwxr-xr-x 11 sasircm sequence 512 May 8 14:47 marrayPlots/ drwxr-xr-x 9 sasircm sequence 512 May 8 14:47 marrayTools/ drwxr-xr-x 14 sasircm sequence 512 May 8 14:47 reposTools/ drwxr-xr-x 12 sasircm sequence 512 May 8 14:47 vsn/ Note: trying a the following command does not work either > memory.limit(size = NA) Error: couldn't find function "memory.limit" > Thank you in advance Johanne Duhaime IRCM duhaimj@ircm.qc.ca tel: (514) 987-5556 fax: (514) 987-5644 www.ircm.qc.ca
affy affy • 1.9k views
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 10.2 years ago
> > library(affy) > Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : > This is not a valid package -- no DESCRIPTION exists > Error in library(affy) : .First.lib failed > > q() It would seem that somehow your installation of the affy package is broken.
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Actually, I get an identical error which seems to be caused by the installation process not installing the DESCRIPTION file. If I install by downloading Bioconductor_1.1.tar.gz and then doing the usual "R CMD INSTALL Bioconductor_1.1.tar.gz", then there are no DESCRIPTION files in the directories. (The same thing happens if I use the getBioC() function). However, if I download the individual tar.gz file for each package, and install each of them individually, then everything works fine. The strange thing is that this did not happen to me about two days after the release of R 1.7.0, when I installed the deb package. A few weeks later I built R from sources, and I just noticed this problem with bioconductor last night. If I now use the original installed package, I get the same error. Note that I have been able to install other packages from CRAN, such as car, gregmisc or e1071, without trouble. Maybe this is a problem with my setup (and with Johanne's set up), but I don't see it, specially since everything works OK when I install the individual Bioc. packages one by one. > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R Ram?n On Thursday 08 May 2003 22:37, Jeff Gentry wrote: > > > library(affy) > > > > Error in library(package, character.only = TRUE, logical = TRUE, > > warn.conflicts = warn.conflicts, : This is not a valid package -- no > > DESCRIPTION exists > > Error in library(affy) : .First.lib failed > > > > > q() > > It would seem that somehow your installation of the affy package is > broken. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz
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On Fri, 9 May 2003, Ramon Diaz wrote: > Actually, I get an identical error which seems to be caused by the > installation process not installing the DESCRIPTION file. I located a problem with our bundle generation code that seems to not get along so well with R-1.7.X. The fixed bundles will find their way to the website in the near future. -J
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@duhaime-johanne-162
Last seen 10.2 years ago
Hellp I have installed the affy package alone. De-install it and Reinstall it without success. I used R CMD INSTALL affyXXX. In the lib directory created by the installation I do have the DESCRIPTION file installed. Thank you -----Message d'origine----- De : Ramon Diaz [mailto:rdiaz@cnio.es] Envoy? : 09-mai-2003 07:30 ? : Jeff Gentry; Duhaime Johanne Cc : bioconductor@stat.math.ethz.ch Objet : Re: [BioC] Bioconductor on Unix: cannot load the library affy Actually, I get an identical error which seems to be caused by the installation process not installing the DESCRIPTION file. If I install by downloading Bioconductor_1.1.tar.gz and then doing the usual "R CMD INSTALL Bioconductor_1.1.tar.gz", then there are no DESCRIPTION files in the directories. (The same thing happens if I use the getBioC() function). However, if I download the individual tar.gz file for each package, and install each of them individually, then everything works fine. The strange thing is that this did not happen to me about two days after the release of R 1.7.0, when I installed the deb package. A few weeks later I built R from sources, and I just noticed this problem with bioconductor last night. If I now use the original installed package, I get the same error. Note that I have been able to install other packages from CRAN, such as car, gregmisc or e1071, without trouble. Maybe this is a problem with my setup (and with Johanne's set up), but I don't see it, specially since everything works OK when I install the individual Bioc. packages one by one. > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R Ram?n On Thursday 08 May 2003 22:37, Jeff Gentry wrote: > > > library(affy) > > > > Error in library(package, character.only = TRUE, logical = TRUE, > > warn.conflicts = warn.conflicts, : This is not a valid package -- no > > DESCRIPTION exists > > Error in library(affy) : .First.lib failed > > > > > q() > > It would seem that somehow your installation of the affy package is > broken. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz
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Dear Johanne, What error message are you getting? I think you are running Linux; could you give more details? Do you get the same error with another version of R? I just tried, and I do not get any errors with R-1.6.2. Could this be a problem with R-1.7.0? If so, then maybe we sould post a summary of this problem to R-help. What seems strange, though, is that not many people seem to be experiencing this problem. Ram?n On Friday 09 May 2003 15:17, Duhaime Johanne wrote: > Hellp > > I have installed the affy package alone. De-install it and Reinstall it > without success. I used R CMD INSTALL affyXXX. In the lib directory created > by the installation I do have the DESCRIPTION file installed. > > Thank you > > > -----Message d'origine----- > De : Ramon Diaz [mailto:rdiaz@cnio.es] > Envoy? : 09-mai-2003 07:30 > ? : Jeff Gentry; Duhaime Johanne > Cc : bioconductor@stat.math.ethz.ch > Objet : Re: [BioC] Bioconductor on Unix: cannot load the library affy > > > Actually, I get an identical error which seems to be caused by the > installation process not installing the DESCRIPTION file. > > If I install by downloading Bioconductor_1.1.tar.gz and then doing the > usual "R CMD INSTALL Bioconductor_1.1.tar.gz", then there are no > DESCRIPTION files in the directories. (The same thing happens if I use the > getBioC() function). > > However, if I download the individual tar.gz file for each package, and > install each of them individually, then everything works fine. > > > The strange thing is that this did not happen to me about two days after > the release of R 1.7.0, when I installed the deb package. A few weeks later > I built R from sources, and I just noticed this problem with bioconductor > last night. > If I now use the original installed package, I get the same error. Note > that I have been able to install other packages from CRAN, such as car, > gregmisc or e1071, without trouble. > > Maybe this is a problem with my setup (and with Johanne's set up), but I > don't see it, specially since everything works OK when I install the > individual Bioc. packages one by one. > > > version > > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 1 > minor 7.0 > year 2003 > month 04 > day 16 > language R > > > Ram?n > > On Thursday 08 May 2003 22:37, Jeff Gentry wrote: > > > > library(affy) > > > > > > Error in library(package, character.only = TRUE, logical = TRUE, > > > warn.conflicts = warn.conflicts, : This is not a valid package -- no > > > DESCRIPTION exists > > > Error in library(affy) : .First.lib failed > > > > > > > q() > > > > It would seem that somehow your installation of the affy package is > > broken. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz
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On Fri, 9 May 2003, Ramon Diaz wrote: > Do you get the same error with another version of R? I just tried, and I do > not get any errors with R-1.6.2. Could this be a problem with R-1.7.0? If so, Is this with the release-bundle or the devel-bundle? > strange, though, is that not many people seem to be experiencing this > problem. Not strange at all. There are not that many people who use the bundle, most people use getBioC() to install Bioconductor. I will look at this and see what the problem is.
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On Friday 09 May 2003 16:40, Jeff Gentry wrote: > Is this with the release-bundle or the devel-bundle? The release one: Bioconductor_1.1.tar.gz > Not strange at all. There are not that many people who use the bundle, > most people use getBioC() to install Bioconductor. But I get the same problem with getBioC(). Thanks, R.
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On Fri, 9 May 2003, Ramon Diaz wrote: > The release one: Bioconductor_1.1.tar.gz Okay. > But I get the same problem with getBioC(). So let me make sure I understand you. Using R-1.7.0 (but not R-1.6.X) using boht the release bundle *and* the getBioC() script you get packages w/o DESCRIPTION files? How do you call getBioC()? -J
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> > So let me make sure I understand you. Using R-1.7.0 (but not > R-1.6.X) using boht the release bundle *and* the getBioC() script you get > packages w/o DESCRIPTION files? Well, that is what I thought. But now I cannot reproduce the behavior with getBioC(), and I am getting other sorts of weird errors, etc. So I am starting to think that my setup is all messed up. I am gonna remove all of my R installations and do a fresh install and will get back to you. > How do you call getBioC()? I "su", and then run R as root. When it starts I do: source("getBioC.R") getBioC() > > -J > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz
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@duhaime-johanne-162
Last seen 10.2 years ago
Hello I succeded in installing BioC with getBioC instead of using the bundle. Thank you for your help -----Message d'origine----- De : Duhaime Johanne Envoy? : 09-mai-2003 09:17 ? : Ramon Diaz; Jeff Gentry Cc : bioconductor@stat.math.ethz.ch Objet : RE: [BioC] Bioconductor on Unix: cannot load the library affy Hellp I have installed the affy package alone. De-install it and Reinstall it without success. I used R CMD INSTALL affyXXX. In the lib directory created by the installation I do have the DESCRIPTION file installed. Thank you -----Message d'origine----- De : Ramon Diaz [mailto:rdiaz@cnio.es] Envoy? : 09-mai-2003 07:30 ? : Jeff Gentry; Duhaime Johanne Cc : bioconductor@stat.math.ethz.ch Objet : Re: [BioC] Bioconductor on Unix: cannot load the library affy Actually, I get an identical error which seems to be caused by the installation process not installing the DESCRIPTION file. If I install by downloading Bioconductor_1.1.tar.gz and then doing the usual "R CMD INSTALL Bioconductor_1.1.tar.gz", then there are no DESCRIPTION files in the directories. (The same thing happens if I use the getBioC() function). However, if I download the individual tar.gz file for each package, and install each of them individually, then everything works fine. The strange thing is that this did not happen to me about two days after the release of R 1.7.0, when I installed the deb package. A few weeks later I built R from sources, and I just noticed this problem with bioconductor last night. If I now use the original installed package, I get the same error. Note that I have been able to install other packages from CRAN, such as car, gregmisc or e1071, without trouble. Maybe this is a problem with my setup (and with Johanne's set up), but I don't see it, specially since everything works OK when I install the individual Bioc. packages one by one. > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R Ram?n On Thursday 08 May 2003 22:37, Jeff Gentry wrote: > > > library(affy) > > > > Error in library(package, character.only = TRUE, logical = TRUE, > > warn.conflicts = warn.conflicts, : This is not a valid package -- no > > DESCRIPTION exists > > Error in library(affy) : .First.lib failed > > > > > q() > > It would seem that somehow your installation of the affy package is > broken. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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