Hi all, I've been trying to install annmap on a windows workstation and have run into a few difficulties (I believe to be specific to the windows installation, which is a bit tricky due to lack of windows binaries for this pre-required packages). I installed MySQL, obtained the annmap database annmap_homo_sapiens_68 and imported it to MySQL as per the instructions provided with the annmap package. I then installed the pre-requisite package RMySQL after shuffling the files libmysql.lib and libmysql.dll appropriately to meet dependencies. I then attempted to install the annmap package from source (a tarball file downloaded from the bioconductor website), but I got some issues regarding the architecture of the install (32 bit vs 64 bit). On my first attempt the version of MySQL downloaded was x64 so I had to install the x64 version of RMySQL, I believe it is this that led to the error printed first below, where loading fails for the i386 arch because RMySQL is not installed in that architecture. So I tried uninstalling MySQL x64 and re-installing a 32 bit version and reinstalling RMySQL in 32 bit only using the command line: "c:\Program Files\R\R-2.15.1\bin\i386\R" CMD INSTALL RMySQL_0.9-3.tar.gz then I re-attempted to install annmap in the 32 bit arch which gave the second error listed. So I think this may be happening because the command: R CMD INSTALL "annmap_1.1.1.tar.gz" fails if it can't install on both 64 and 32 bit rather than just one of the two, and my version of MySQL can only be one or the other. Is there a way to force R to only install the 32 bit is 64 bit version and not both, or is there an easy way to install this that I'm not seeing? Thanks very much! Best wishes, Chris -- output of sessionInfo(): #Error if using x64 version of MySQL and RMySQL > install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",re pos=NULL,type="source") Installing package(s) into ???C:/Users/ucbpban/Documents/R/win- library/2.15??? (as ???lib??? is unspecified) * installing *source* package 'annmap' ... ** R ** inst ** preparing package for lazy loading MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 ** help *** installing help indices ** building package indices ** installing vignettes 'INSTALL.Rnw' 'annmap.Rnw' 'cookbook.Rnw' ** testing if installed package can be loaded *** arch - i386 MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 Error : .onLoad failed in loadNamespace() for 'RMySQL', details: call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) error: DLL 'RMySQL' not found: maybe not installed for this architecture? Error: loading failed Execution halted *** arch - x64 MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 ERROR: loading failed for 'i386' * removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' Warning in install.packages : running command 'C:/PROGRA~1/R/R-215~1.2/bin/x64/R CMD INSTALL -l "C:/Users/ucbpban/Documents/R/win-library/2.15" "C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz"' had status 1 Warning in install.packages : installation of package ???C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz??? had non-zero exit status #Error if using x32 version of MySQL and RMySQL > install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",ty pe="source") Installing package(s) into 'C:/Users/ucbpban/Documents/R/win- library/2.15' (as 'lib' is unspecified) inferring 'repos = NULL' from the file name * installing *source* package 'annmap' ... ** R ** inst ** preparing package for lazy loading MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 ** help *** installing help indices ** building package indices ** installing vignettes 'INSTALL.Rnw' 'annmap.Rnw' 'cookbook.Rnw' ** testing if installed package can be loaded *** arch - i386 MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 *** arch - x64 MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 Error : .onLoad failed in loadNamespace() for 'RMySQL', details: call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) error: DLL 'RMySQL' not found: maybe not installed for this architecture? Error: loading failed Execution halted ERROR: loading failed for 'x64' * removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' Warning message: In install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz", : installation of package 'C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz' had non-zero exit status > -- Sent via the guest posting facility at bioconductor.org.

On Thu, Jan 17, 2013 at 8:38 AM, Chris Banerji [guest] <guest at="" bioconductor.org=""> wrote: > > Hi all, > > I've been trying to install annmap on a windows workstation and have run into a few difficulties (I believe to be specific to the windows installation, which is a bit tricky due to lack of windows binaries for this pre-required packages). > > I installed MySQL, obtained the annmap database annmap_homo_sapiens_68 and imported it to MySQL as per the instructions provided with the annmap package. I then installed the pre-requisite package RMySQL after shuffling the files libmysql.lib and libmysql.dll appropriately to meet dependencies. > > I then attempted to install the annmap package from source (a tarball file downloaded from the bioconductor website), but I got some issues regarding the architecture of the install (32 bit vs 64 bit). > > On my first attempt the version of MySQL downloaded was x64 so I had to install the x64 version of RMySQL, I believe it is this that led to the error printed first below, where loading fails for the i386 arch because RMySQL is not installed in that architecture. > > So I tried uninstalling MySQL x64 and re-installing a 32 bit version and reinstalling RMySQL in 32 bit only using the command line: > > "c:\Program Files\R\R-2.15.1\bin\i386\R" CMD INSTALL RMySQL_0.9-3.tar.gz > > then I re-attempted to install annmap in the 32 bit arch which gave the second error listed. > > So I think this may be happening because the command: > > R CMD INSTALL "annmap_1.1.1.tar.gz" fails if it can't install on both 64 and 32 bit rather than just one of the two, and my version of MySQL can only be one or the other. > > Is there a way to force R to only install the 32 bit is 64 bit version and not both, or is there an easy way to install this that I'm not seeing? > R CMD INSTALL --no-multiarch RMySQL_0.9-3.tar.gz Dan > Thanks very much! > Best wishes, > Chris > > -- output of sessionInfo(): > > #Error if using x64 version of MySQL and RMySQL >> install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",r epos=NULL,type="source") > Installing package(s) into ???C:/Users/ucbpban/Documents/R/win- library/2.15??? > (as ???lib??? is unspecified) > * installing *source* package 'annmap' ... > ** R > ** inst > ** preparing package for lazy loading > MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 > ** help > *** installing help indices > ** building package indices > ** installing vignettes > 'INSTALL.Rnw' > 'annmap.Rnw' > 'cookbook.Rnw' > ** testing if installed package can be loaded > *** arch - i386 > MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 > Error : .onLoad failed in loadNamespace() for 'RMySQL', details: > call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) > error: DLL 'RMySQL' not found: maybe not installed for this architecture? > Error: loading failed > Execution halted > *** arch - x64 > MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 > ERROR: loading failed for 'i386' > * removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' > Warning in install.packages : > running command 'C:/PROGRA~1/R/R-215~1.2/bin/x64/R CMD INSTALL -l "C:/Users/ucbpban/Documents/R/win-library/2.15" "C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz"' had status 1 > Warning in install.packages : > installation of package ???C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz??? had non-zero exit status > > #Error if using x32 version of MySQL and RMySQL >> install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",t ype="source") > Installing package(s) into 'C:/Users/ucbpban/Documents/R/win- library/2.15' > (as 'lib' is unspecified) > inferring 'repos = NULL' from the file name > * installing *source* package 'annmap' ... > ** R > ** inst > ** preparing package for lazy loading > MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 > ** help > *** installing help indices > ** building package indices > ** installing vignettes > 'INSTALL.Rnw' > 'annmap.Rnw' > 'cookbook.Rnw' > ** testing if installed package can be loaded > *** arch - i386 > MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 > *** arch - x64 > MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 > Error : .onLoad failed in loadNamespace() for 'RMySQL', details: > call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) > error: DLL 'RMySQL' not found: maybe not installed for this architecture? > Error: loading failed > Execution halted > ERROR: loading failed for 'x64' > * removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' > Warning message: > In install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz", : > installation of package 'C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz' had non-zero exit status >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Chris, This sounds like a problem with the RMySQL installation on your machine. Can you verify it works before trying to install annmap? Unfortunately, we don't have a Windows machine with enough horsepower to build, run or test annmap on the Windows platform, and that (and that I had some problems getting RMySQL up and running on Windows) is why I marked the project to not build a Windows binary. There is a post here[1] on StackOverflow which explains the steps that should be necessary to get RMySQL installed correctly. But as I said, I haven't tried them :-( Tim 1: http://stackoverflow.com/questions/5223113/using-mysql-in-r-for- windows/523 0980#5230980 On 17/01/2013 16:38, "Chris Banerji [guest]" <guest at="" bioconductor.org=""> wrote: > >Hi all, > >I've been trying to install annmap on a windows workstation and have run >into a few difficulties (I believe to be specific to the windows >installation, which is a bit tricky due to lack of windows binaries for >this pre-required packages). > >I installed MySQL, obtained the annmap database annmap_homo_sapiens_68 >and imported it to MySQL as per the instructions provided with the annmap >package. I then installed the pre-requisite package RMySQL after >shuffling the files libmysql.lib and libmysql.dll appropriately to meet >dependencies. > >I then attempted to install the annmap package from source (a tarball >file downloaded from the bioconductor website), but I got some issues >regarding the architecture of the install (32 bit vs 64 bit). > >On my first attempt the version of MySQL downloaded was x64 so I had to >install the x64 version of RMySQL, I believe it is this that led to the >error printed first below, where loading fails for the i386 arch because >RMySQL is not installed in that architecture. > >So I tried uninstalling MySQL x64 and re-installing a 32 bit version and >reinstalling RMySQL in 32 bit only using the command line: > >"c:\Program Files\R\R-2.15.1\bin\i386\R" CMD INSTALL RMySQL_0.9-3.tar.gz > >then I re-attempted to install annmap in the 32 bit arch which gave the >second error listed. > >So I think this may be happening because the command: > >R CMD INSTALL "annmap_1.1.1.tar.gz" fails if it can't install on both 64 >and 32 bit rather than just one of the two, and my version of MySQL can >only be one or the other. > >Is there a way to force R to only install the 32 bit is 64 bit version >and not both, or is there an easy way to install this that I'm not seeing? > >Thanks very much! >Best wishes, >Chris > > -- output of sessionInfo(): > >#Error if using x64 version of MySQL and RMySQL >> >>install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",re pos=N >>ULL,type="source") >Installing package(s) into >???C:/Users/ucbpban/Documents/R/win-library/2.15??? >(as ???lib??? is unspecified) >* installing *source* package 'annmap' ... >** R >** inst >** preparing package for lazy loading >MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 >** help >*** installing help indices >** building package indices >** installing vignettes > 'INSTALL.Rnw' > 'annmap.Rnw' > 'cookbook.Rnw' >** testing if installed package can be loaded >*** arch - i386 >MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 >Error : .onLoad failed in loadNamespace() for 'RMySQL', details: > call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) > error: DLL 'RMySQL' not found: maybe not installed for this >architecture? >Error: loading failed >Execution halted >*** arch - x64 >MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5 >ERROR: loading failed for 'i386' >* removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' >Warning in install.packages : > running command 'C:/PROGRA~1/R/R-215~1.2/bin/x64/R CMD INSTALL -l >"C:/Users/ucbpban/Documents/R/win-library/2.15" >"C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz"' had status 1 >Warning in install.packages : > installation of package >???C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz??? had non-zero exit >status > >#Error if using x32 version of MySQL and RMySQL >> >>install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",ty pe="s >>ource") >Installing package(s) into 'C:/Users/ucbpban/Documents/R/win- library/2.15' >(as 'lib' is unspecified) >inferring 'repos = NULL' from the file name >* installing *source* package 'annmap' ... >** R >** inst >** preparing package for lazy loading >MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 >** help >*** installing help indices >** building package indices >** installing vignettes > 'INSTALL.Rnw' > 'annmap.Rnw' > 'cookbook.Rnw' >** testing if installed package can be loaded >*** arch - i386 >MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 >*** arch - x64 >MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5 >Error : .onLoad failed in loadNamespace() for 'RMySQL', details: > call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll) > error: DLL 'RMySQL' not found: maybe not installed for this >architecture? >Error: loading failed >Execution halted >ERROR: loading failed for 'x64' >* removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap' >Warning message: >In install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz", : > installation of package >'C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz' had non-zero exit status >> > > >-- >Sent via the guest posting facility at bioconductor.org. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor ________________________________ This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. 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