Re: [Bioc-devel] Installing EBImage with custom packages dir?
You can always use biocLite(pkg , lib="path/to/library") . The lib path in biocLite defaults to the .libPaths()[1]. When you do .libPaths() upon opening R does your path appear that you set with the environment variables? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Guillaume MULLER <g...@presans.com> Sent: Tuesday, April 11, 2017 8:28:34 AM To: Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Installing EBImage with custom packages dir? Hi, Thanks for your answer. The R_LIBS and R_LIBS_USER environment variables are already set in my ~/.Renviron . They point to the correct location. But this latter is not selected when installing packages with biocLite()... Cheers GM -- Guillaume MULLER, PhD PRESANS - Remix Coworking - L'Appart 57 rue de Turbigo 75003 Paris France http://www.presans.com http://feeds.feedburner.com/OYI/fr This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Installing EBImage with custom packages dir?
Hi, Thanks for your answer. The R_LIBS and R_LIBS_USER environment variables are already set in my ~/.Renviron . They point to the correct location. But this latter is not selected when installing packages with biocLite()... Cheers GM -- Guillaume MULLER, PhD PRESANS - Remix Coworking - L'Appart 57 rue de Turbigo 75003 Paris France http://www.presans.com http://feeds.feedburner.com/OYI/fr ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Installing EBImage with custom packages dir?
If you are able to set environment variables or have a .bash_aliases, you could set the R_LIBS or R_LIBS_USER environment variables to your desired path "~/.R/x86_64-pc-linux-gnu-library/3.1.2". When these are set it should become the default path in .libPaths() when you start R. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Guillaume MULLER <g...@presans.com> Sent: Monday, April 3, 2017 5:45:22 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Installing EBImage with custom packages dir? Hi, I've been installing EBImage several time these past months on multiple machines, using instructions at: http://bioconductor.org/packages/release/bioc/html/EBImage.html. I've noticed a few strange things with the installer: - When the installer installs the dependencies and one of them fails (e.g. "tiff" or "png", because the headers are not installed on the system), and I run again biocLite("EBImage"), then even the dependencies that previously installed successfully (I saw the "DONE (xxx)" line in the logs) are re-downloaded and re-installed... - The script asks if I want to upgrade my packages. If I says yes, then the system-wide installation fails because I'm not root, thus the biocLite() asks if I want to install the packages in my "personal library". If I answer "yes", it installs the packages in the default personal library location ("~/R/x86_64-pc-linux-gnu-library/3.2"), whereas I've hardcoded my personal library location by using (.libPaths("~/.R/x86_64-pc-linux-gnu-library/3.1.2" in my .Rprofile)... Also, I'm not sure the script does not takes into account the packages already installed installed in my personal library, thus redundantly (re)-installs some packages in the default location. Is there any work-around so that I don't have to move all the (redundantly) installed packages into my actual personal library? Cheers GM -- Guillaume MULLER, PhD PRESANS - Remix Coworking - L'Appart 57 rue de Turbigo 75003 Paris France http://www.presans.com http://feeds.feedburner.com/OYI/fr ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Installing EBImage with custom packages dir?
Hi, I've been installing EBImage several time these past months on multiple machines, using instructions at: http://bioconductor.org/packages/release/bioc/html/EBImage.html. I've noticed a few strange things with the installer: - When the installer installs the dependencies and one of them fails (e.g. "tiff" or "png", because the headers are not installed on the system), and I run again biocLite("EBImage"), then even the dependencies that previously installed successfully (I saw the "DONE (xxx)" line in the logs) are re-downloaded and re-installed... - The script asks if I want to upgrade my packages. If I says yes, then the system-wide installation fails because I'm not root, thus the biocLite() asks if I want to install the packages in my "personal library". If I answer "yes", it installs the packages in the default personal library location ("~/R/x86_64-pc-linux-gnu-library/3.2"), whereas I've hardcoded my personal library location by using (.libPaths("~/.R/x86_64-pc-linux-gnu-library/3.1.2" in my .Rprofile)... Also, I'm not sure the script does not takes into account the packages already installed installed in my personal library, thus redundantly (re)-installs some packages in the default location. Is there any work-around so that I don't have to move all the (redundantly) installed packages into my actual personal library? Cheers GM -- Guillaume MULLER, PhD PRESANS - Remix Coworking - L'Appart 57 rue de Turbigo 75003 Paris France http://www.presans.com http://feeds.feedburner.com/OYI/fr ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel