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David Kremelberg

2014-Feb-04 06:12 UTC

[R] Trying to install package for LMER, getting a ton of errors

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]]

Pascal Oettli

2014-Feb-04 07:16 UTC

head link

[R] Trying to install package for LMER, getting a ton of errors

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

Steve Lianoglou

2014-Feb-04 07:17 UTC

head link

[R] Trying to install package for LMER, getting a ton of errors

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

R help - Feb 2014 - Trying to install package for LMER, getting a ton of errors

[R] Trying to install package for LMER, getting a ton of errors

[R] Trying to install package for LMER, getting a ton of errors

[R] Trying to install package for LMER, getting a ton of errors