Question: Bioconductor Install Problems
gravatar for Smith, Troy NIH/NCI
14.9 years ago by
Smith, Troy NIH/NCI10 wrote:
Hello all, We have installed R-2.0.0 on a Red Hat ES 3.0 server and have been trying to install all of the Bioconductor pkgs for a few days using the following methods: >getBioC >update.packages2() >install.packages2() #R CMD INSTALL package name We continually encounter the same two issues. An example of the first issue when trying to install KEGGSOAP: [1] "Attempting to download KEGGSOAP from" [1] "Download complete." [1] "Installing KEGGSOAP" * Installing *source* package 'KEGGSOAP' ... ** R ** save image Loading required package: XML Loading required package: SSOAP Loading required package: RCurl Error in library.dynam(lib, package, package.lib) : shared library 'RCurl' not found In addition: Warning messages: 1: Package 'RCurl' contains no R code in: loadNamespace(package, c(which.lib.loc, lib.loc)) 2: S3 method(s) '[<-.CURLOptions', '[[<-.CURLOptions' were declared in NAMESPACE but not found Error: package 'RCurl' could not be loaded Execution halted ERROR: execution of package source for 'KEGGSOAP' failed >From URL: KEGGSOAP version 0.6.5 Warning message: Installation of package KEGGSOAP had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) We have tried upgrading from R1.9.1 (using Bioconductor 1.4) to R2.0.0 to R2.0.1. We have tried fresh installs of R2.0.0 and R2.0.1 on this server, as well as alternate Red Hat ES 3 boxes. The second issue involves RGraphviz when we use >getBioC("all"). The following message pops up: Package RGraphviz requires special libraries to be installed. We are pointed to the faq on <http:""/> , which states Graphviz 1.12 or above required. The system currently has the following Graphviz packages installed: graphviz-devel-1.16-1 graphviz-tcl-1.16-1 graphviz-1.16-1 We have also tried more recent versions, both RPM and from source. Our current expertise of both R and Bioconductor is limited, and our developers who actually use these applications are investigating on their own, however we though we would ask the experts. Any assistance you are able to provide is greatly appreciated. Thanks Troy Troy D Smith Network Engineer NCICB/LPG Systems Group Contractor, Terrapin Systems Terrapin Systems 6905 Rockledge Drive, Suite 200 Bethesda, MD 20817 301.530.9106 x323 Corporate Voice 301.530.9105 Corporate Fax <https:""/> Technology Driven. People Oriented. Voted on of 50 "Great Places to Work" - The Washingtonian [[alternative HTML version deleted]]
rgraphviz keggsoap • 519 views
ADD COMMENTlink modified 14.9 years ago by Seth Falcon7.4k • written 14.9 years ago by Smith, Troy NIH/NCI10
Answer: Bioconductor Install Problems
gravatar for Seth Falcon
14.9 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi Troy, I think the problems you are running into are related to the fact that some R packages depend on certain libraries being installed at the system level. The errors for KEGGSOAP appear to really be errors with RCurl. RCurl requires libcurl. On an rpm based system, you will need to install the libcurl rpm as well as the libcurl-devel rpm. The message from Rgraphviz is because you need to install the graphviz libs. Also, I recommend that you start with R-patched (latest bug fixed version of R) or at least R 2.0.1. HTH, + seth
ADD COMMENTlink written 14.9 years ago by Seth Falcon7.4k
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