Hi, I work with Windows XP. I recently updated to R v.2.7 and Bioconductor v.2.2, and am now having trouble loading libraries of packages that appear to have been installed successfully. An example for the workflow and error message I get when I try to load the library for the “RMySQL” package follows: utils:::menuInstallPkgs() trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/RMySQL_0.6 -0.zip' ... package 'RMySQL' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\YYYYYY\Local Settings\Temp\RtmpF3NdQe\downloaded_packages updating HTML package descriptions > library(RMySQL) Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'RMySQL' I thought it was simply an issue with the RMySQL .dll (as discussed at http://134.148.236.121/R/e2/help/07/10/28144.html), but I get an identical error with the xps package, even though the xps.dll file is present in the C:\Program Files\R\R-2.7.1\library\xps\libs folder. Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/xps/libs/xps.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'xps' This error does not appear for all downloaded packages – for example, libraries for the “affy”, “multtest” and “plier” packages install fine. Can anyone tell me why R can’t “find” the RMySQL.dll & xps.dll files, and how to bypass this issue? Any help would be much appreciated! Regards, Marie Marie Alles Garvan Institute of Medical Research 384 Victoria Street, Darlinghust, Sydney, NSW 2010, AUSTRALIA [[alternative HTML version deleted]]

Hi Marie -- Marie Chehani Alles <m.alles at="" garvan.org.au=""> writes: > Hi, > I work with Windows XP. I recently updated to R > v.2.7 and Bioconductor v.2.2, and am now having > trouble loading libraries of packages that appear to > have been installed successfully. > > An example for the workflow and error message I get > when I try to load the library for the ?RMySQL? > package follows: > > utils:::menuInstallPkgs() > trying URL > 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/RMySQL_0 .6-0.zip' > ... > package 'RMySQL' successfully unpacked and MD5 sums > checked > > The downloaded packages are in > C:\Documents and Settings\YYYYYY\Local > Settings\Temp\RtmpF3NdQe\downloaded_packages > updating HTML package descriptions > >> library(RMySQL) > Error in inDL(x, as.logical(local), as.logical(now), > ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': > LoadLibrary failure: The specified module could not > be found. Both RMySQL and xps depend on additional software, and the error message is probably trying to say that errors in the external software configuration made it impossible to load the R package. For RMySQL, it looks like mysql has to be installed, and libmysql.dll on the PATH variable of your system (the elaborate solution of copying libmysql.dll from another distribution suggested in the email thread does not seem like a good idea to me; install MySQL, find libmysql.dll in the installation, add the path to the containing folder to the environment variable PATH). xps requires ROOT. I do not have experience with that, but again the package has a README file that details steps required for installation and on configuration on Windows. Hope that helps, Martin > Error: package/namespace load failed for 'RMySQL' > > I thought it was simply an issue with the RMySQL > .dll (as discussed at > http://134.148.236.121/R/e2/help/07/10/28144.html), > but I get an identical error with the xps package, > even though the xps.dll file is present in the > C:\Program Files\R\R-2.7.1\library\xps\libs folder. > > Error in inDL(x, as.logical(local), as.logical(now), > ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.1/library/xps/libs/xps.dll': > LoadLibrary failure: The specified module could not > be found. > Error: package/namespace load failed for 'xps' > This error does not appear for all downloaded > packages ? for example, libraries for the > ?affy?, ?multtest? and ?plier? packages > install fine. > > Can anyone tell me why R can?t ?find? the > RMySQL.dll & xps.dll files, and how to bypass this > issue? Any help would be much appreciated! > > Regards, > Marie > > Marie Alles > Garvan Institute of Medical Research > 384 Victoria Street, Darlinghust, Sydney, NSW 2010, > AUSTRALIA > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

would you please include a sessionInfo() result after triggering the errors? my initial guess is that there is a problem with the installation of R 2.7 if the following is accurate 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': the 27~1.1 seems strange to me. send your sessionInfo and i will attempt to replicate --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Thu, 3 Jul 2008, Marie Chehani Alles wrote: > Hi, I work with Windows XP. I recently updated to R v.2.7 and Bioconductor v.2.2, and am now having trouble loading libraries of packages that appear to have been installed successfully. An example for the workflow and error message I get when I try to load the library for the ???RMySQL??? package follows: utils:::menuInstallPkgs() trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/RMySQL_0.6 -0.zip' ... package 'RMySQL' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\YYYYYY\Local Settings\Temp\RtmpF3NdQe\downloaded_packages updating HTML package descriptions > library(RMySQL) Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'RMySQL' I thought it was simply an issue with the RMySQL .dll (as discussed at http://134.148.236.121/R/e2/help/07/10/28144.html), but I get an identical error with the xps package, even though the xps.dll file is present in the C:\Program Files\R\R-2.7.1\library\xps\libs folder. Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/xps/libs/xps.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'xps' This error does not appear for all downloaded packages ??? for example, libraries for the ???affy???, ???multtest??? and ???plier??? packages install fine. Can anyone tell me why R can???t ???find??? the RMySQL.dll & xps.dll files, and how to bypass this issue? Any help would be much appreciated! Regards, Marie Marie Alles Garvan Institute of Medical Research 384 Victoria Street, Darlinghust, Sydney, NSW 2010, AUSTRALIA [[alternative HTML version deleted]] -------------- next part -------------- The information transmitted in this electronic communica...{{dropped:18}}

Hi Martin & Vince, Thank you for your replies. I tried Martin?s suggestion which was to add the path to a downloaded libmySQL.dll file to the PATH variable in my environment variables, and RMySQL loaded perfectly. I now see that xps needs the ?libCore.dll? file (from ROOT) before it can load. Thanks again! Marie Marie Alles Garvan Institute of Medical Research 384 Victoria Street, Darlinghust, Sydney, NSW 2010, AUSTRALIA ---- Original message ---- >Date: Thu, 03 Jul 2008 05:26:05 -0700 >From: Martin Morgan <mtmorgan at="" fhcrc.org=""> >Subject: Re: [BioC] LoadLibrary failures when loading RMySQL and xps packages >To: m.alles at garvan.org.au >Cc: bioconductor at stat.math.ethz.ch > >Hi Marie -- > >Marie Chehani Alles <m.alles at="" garvan.org.au=""> writes: > >> Hi, >> I work with Windows XP. I recently updated to R >> v.2.7 and Bioconductor v.2.2, and am now having >> trouble loading libraries of packages that appear to >> have been installed successfully. >> >> An example for the workflow and error message I get >> when I try to load the library for the ?RMySQL? >> package follows: >> >> utils:::menuInstallPkgs() >> trying URL >> 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/RMySQL_ 0.6-0.zip' >> ... >> package 'RMySQL' successfully unpacked and MD5 sums >> checked >> >> The downloaded packages are in >> C:\Documents and Settings\YYYYYY\Local >> Settings\Temp\RtmpF3NdQe\downloaded_packages >> updating HTML package descriptions >> >>> library(RMySQL) >> Error in inDL(x, as.logical(local), as.logical(now), >> ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': >> LoadLibrary failure: The specified module could not >> be found. > >Both RMySQL and xps depend on additional software, and the error >message is probably trying to say that errors in the external software >configuration made it impossible to load the R package. > >For RMySQL, it looks like mysql has to be installed, and libmysql.dll >on the PATH variable of your system (the elaborate solution of copying >libmysql.dll from another distribution suggested in the email thread >does not seem like a good idea to me; install MySQL, find libmysql.dll >in the installation, add the path to the containing folder to the >environment variable PATH). > >xps requires ROOT. I do not have experience with that, but again the >package has a README file that details steps required for installation >and on configuration on Windows. > >Hope that helps, > >Martin > >> Error: package/namespace load failed for 'RMySQL' >> >> I thought it was simply an issue with the RMySQL >> .dll (as discussed at >> http://134.148.236.121/R/e2/help/07/10/28144.html), >> but I get an identical error with the xps package, >> even though the xps.dll file is present in the >> C:\Program Files\R\R-2.7.1\library\xps\libs folder. >> >> Error in inDL(x, as.logical(local), as.logical(now), >> ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-27~1.1/library/xps/libs/xps.dll': >> LoadLibrary failure: The specified module could not >> be found. >> Error: package/namespace load failed for 'xps' >> This error does not appear for all downloaded >> packages ? for example, libraries for the >> ?affy?, ?multtest? and ?plier? packages >> install fine. >> >> Can anyone tell me why R can?t ?find? the >> RMySQL.dll & xps.dll files, and how to bypass this >> issue? Any help would be much appreciated! >> >> Regards, >> Marie >> >> Marie Alles >> Garvan Institute of Medical Research >> 384 Victoria Street, Darlinghust, Sydney, NSW 2010, >> AUSTRALIA >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >-- >Martin Morgan >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M2 B169 >Phone: (206) 667-2793