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Trying to install package for LMER, getting a ton of errors
3 messages · David Kremelberg, Pascal Oettli, Steve Lianoglou
Hello, I am wondering why you are trying to install from source on your Windows machine. Is there any reason for you to not use Windows binaries? Regards, Pascal
On 4 February 2014 15:12, David Kremelberg <david.kremelberg at gmail.com> wrote:
Hi all, trying to run a linear mixed-effects model in R. Getting a ton of errors when trying to install the lme4 package (see below). I thought it was because my version of R was old, I just updated it, same exact problem, plus tried the install on the 32 and 64 bit versions. Any help appreciated.
install.packages(type="source")
--- Please select a CRAN mirror for use in this session --- also installing the dependencies 'Matrix', 'minqa', 'Rcpp', 'RcppEigen' trying URL 'http://cran.at.r-project.org/src/contrib/Matrix_1.1-2.tar.gz' Content type 'application/x-gzip' length 1635852 bytes (1.6 Mb) opened URL downloaded 1.6 Mb trying URL 'http://cran.at.r-project.org/src/contrib/minqa_1.2.2.tar.gz' Content type 'application/x-gzip' length 53162 bytes (51 Kb) opened URL downloaded 51 Kb trying URL 'http://cran.at.r-project.org/src/contrib/Rcpp_0.11.0.tar.gz' Content type 'application/x-gzip' length 1998844 bytes (1.9 Mb) opened URL downloaded 1.9 Mb trying URL ' http://cran.at.r-project.org/src/contrib/RcppEigen_0.3.2.0.2.tar.gz' Content type 'application/x-gzip' length 1251504 bytes (1.2 Mb) opened URL downloaded 1.2 Mb trying URL 'http://cran.at.r-project.org/src/contrib/lme4_1.0-6.tar.gz' Content type 'application/x-gzip' length 2706277 bytes (2.6 Mb) opened URL downloaded 2.6 Mb * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'Matrix' * removing 'C:/Program Files/R/R-3.0.2/library/Matrix' * restoring previous 'C:/Program Files/R/R-3.0.2/library/Matrix' * installing *source* package 'Rcpp' ... ** package 'Rcpp' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'Rcpp' * removing 'C:/Program Files/R/R-3.0.2/library/Rcpp' * restoring previous 'C:/Program Files/R/R-3.0.2/library/Rcpp' * installing *source* package 'minqa' ... ** package 'minqa' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'minqa' * removing 'C:/Program Files/R/R-3.0.2/library/minqa' * installing *source* package 'RcppEigen' ... ** package 'RcppEigen' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'RcppEigen' * removing 'C:/Program Files/R/R-3.0.2/library/RcppEigen' ERROR: dependencies 'minqa', 'RcppEigen' are not available for package 'lme4' * removing 'C:/Program Files/R/R-3.0.2/library/lme4' The downloaded source packages are in 'C:\Users\Master\AppData\Local\Temp\RtmpyChM99\downloaded_packages' Warning messages: 1: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/Matrix_1.1-2.tar.gz' had status 1 2: In install.packages(type = "source") : installation of package 'Matrix' had non-zero exit status 3: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/Rcpp_0.11.0.tar.gz' had status 1 4: In install.packages(type = "source") : installation of package 'Rcpp' had non-zero exit status 5: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/minqa_1.2.2.tar.gz' had status 1 6: In install.packages(type = "source") : installation of package 'minqa' had non-zero exit status 7: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/RcppEigen_0.3.2.0.2.tar.gz' had status 1 8: In install.packages(type = "source") : installation of package 'RcppEigen' had non-zero exit status 9: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/lme4_1.0-6.tar.gz' had status 1 10: In install.packages(type = "source") : installation of package 'lme4' had non-zero exit status [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan
Hi, On Mon, Feb 3, 2014 at 10:12 PM, David Kremelberg
<david.kremelberg at gmail.com> wrote:
Hi all, trying to run a linear mixed-effects model in R. Getting a ton of errors when trying to install the lme4 package (see below). I thought it was because my version of R was old, I just updated it, same exact problem, plus tried the install on the 32 and 64 bit versions. Any help appreciated.
install.packages(type="source")
You might try not specifying `type="source"` side-step this issue. I don't run windows, but I believe that unless you've done something "special," then R should default to installing binary versions of these packages, so the compilation problems you are having would go away. If I had to guess at what's causing the problems you are having compiling these packages, it'd be that you don't have a sane build environment set up on your windows machine. Since the packages you are installing require C/C++ compilation, you might need extra care here (ie. you need the correct version of GCC installed). It looks like your first points of reference should be here: http://cran.r-project.org/bin/windows/Rtools/ http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset HTH, -steve
--- Please select a CRAN mirror for use in this session --- also installing the dependencies 'Matrix', 'minqa', 'Rcpp', 'RcppEigen' trying URL 'http://cran.at.r-project.org/src/contrib/Matrix_1.1-2.tar.gz' Content type 'application/x-gzip' length 1635852 bytes (1.6 Mb) opened URL downloaded 1.6 Mb trying URL 'http://cran.at.r-project.org/src/contrib/minqa_1.2.2.tar.gz' Content type 'application/x-gzip' length 53162 bytes (51 Kb) opened URL downloaded 51 Kb trying URL 'http://cran.at.r-project.org/src/contrib/Rcpp_0.11.0.tar.gz' Content type 'application/x-gzip' length 1998844 bytes (1.9 Mb) opened URL downloaded 1.9 Mb trying URL ' http://cran.at.r-project.org/src/contrib/RcppEigen_0.3.2.0.2.tar.gz' Content type 'application/x-gzip' length 1251504 bytes (1.2 Mb) opened URL downloaded 1.2 Mb trying URL 'http://cran.at.r-project.org/src/contrib/lme4_1.0-6.tar.gz' Content type 'application/x-gzip' length 2706277 bytes (2.6 Mb) opened URL downloaded 2.6 Mb * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'Matrix' * removing 'C:/Program Files/R/R-3.0.2/library/Matrix' * restoring previous 'C:/Program Files/R/R-3.0.2/library/Matrix' * installing *source* package 'Rcpp' ... ** package 'Rcpp' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'Rcpp' * removing 'C:/Program Files/R/R-3.0.2/library/Rcpp' * restoring previous 'C:/Program Files/R/R-3.0.2/library/Rcpp' * installing *source* package 'minqa' ... ** package 'minqa' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'minqa' * removing 'C:/Program Files/R/R-3.0.2/library/minqa' * installing *source* package 'RcppEigen' ... ** package 'RcppEigen' successfully unpacked and MD5 sums checked ** libs *** arch - i386 ERROR: compilation failed for package 'RcppEigen' * removing 'C:/Program Files/R/R-3.0.2/library/RcppEigen' ERROR: dependencies 'minqa', 'RcppEigen' are not available for package 'lme4' * removing 'C:/Program Files/R/R-3.0.2/library/lme4' The downloaded source packages are in 'C:\Users\Master\AppData\Local\Temp\RtmpyChM99\downloaded_packages' Warning messages: 1: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/Matrix_1.1-2.tar.gz' had status 1 2: In install.packages(type = "source") : installation of package 'Matrix' had non-zero exit status 3: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/Rcpp_0.11.0.tar.gz' had status 1 4: In install.packages(type = "source") : installation of package 'Rcpp' had non-zero exit status 5: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/minqa_1.2.2.tar.gz' had status 1 6: In install.packages(type = "source") : installation of package 'minqa' had non-zero exit status 7: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/RcppEigen_0.3.2.0.2.tar.gz' had status 1 8: In install.packages(type = "source") : installation of package 'RcppEigen' had non-zero exit status 9: running command '"C:/PROGRA~1/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.2\library" C:\Users\Master\AppData\Local\Temp\RtmpyChM99/downloaded_packages/lme4_1.0-6.tar.gz' had status 1 10: In install.packages(type = "source") : installation of package 'lme4' had non-zero exit status [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Steve Lianoglou Computational Biologist Genentech