date:20161130

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Rodriguez Martinez, Andrea

Thanks very much!

From: Nitesh 
Sent: 30 November 2016 16:39:34
To: Rodriguez Martinez, Andrea; Kasper Daniel Hansen
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel 
in mac

This should help:

https://cran.r-project.org/bin/macosx/tools/

On Wed, 30 Nov 2016 at 11:29 Rodriguez Martinez, Andrea 
>
 wrote:
Thanks very much for the clarification.

Best wishes,

Andrea

From: Kasper Daniel Hansen 
>
Sent: 30 November 2016 16:26:10
To: Rodriguez Martinez, Andrea
Cc: Vincent Carey; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel 
in mac

You are not set up to compile from source.  Specifically, you're missing a 
fortran compiler (gfortran)

On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea 
>>
 wrote:

This is all I get:

> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> biocLite("MWASTools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable) 
(2016-10-26 r71594).
Installing package(s) �MWASTools�
also installing the dependencies �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
  cannot download all files
Packages which are only available in source form, and may need compilation of 
C/C++/Fortran:
  �minqa� �RcppEigen� �lme4� �SparseM� �quantreg� �irlba� �igraph�
Do you want to attempt to install these from sources?
y/n: y
trying URL 
'https://bioconductor.org/packages/3.5/bioc/bin/macosx/mavericks/contrib/3.4/MWASTools_0.99.10.tgz'
Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
==
downloaded 2.1 MB

The downloaded binary packages are in
/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn/T//Rtmp79qF9E/downloaded_packages
installing the source packages �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==
downloaded 52 KB

trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.tar.gz'
Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
==
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
==
downloaded 3.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
Content type 'application/x-gzip' length 737540 bytes (720 KB)
==
downloaded 720 KB

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
==
downloaded 161 KB

trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
==
downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
Content type 'application/x-gzip' length 218471 bytes (213 KB)
==
downloaded 213 KB

trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
==
downloaded 608 KB

trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
==
downloaded 3.2 MB

* installing *source* package �minqa� ...
** package �minqa� successfully unpacked and MD5 sums checked
** libs
gfortran-4.8   -fPIC  -g -O2  -c altmov.f -o altmov.o
make: gfortran-4.8: No such file or directory
make: *** [altmov.o] Error 1
ERROR: compilation failed for package �minqa�
* removing 
�/Library/Frameworks/R.framework/Versions/3.4/Resources/library/minqa�
* installing *source* package �RcppEigen� ...
** package �RcppEigen� successfully unpacked and MD5 sums checked
** libs
clang++

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Rodriguez Martinez, Andrea

This is all I get:

> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> biocLite("MWASTools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable) 
(2016-10-26 r71594).
Installing package(s) �MWASTools�
also installing the dependencies �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
  cannot download all files
Packages which are only available in source form, and may need compilation of 
C/C++/Fortran:
  �minqa� �RcppEigen� �lme4� �SparseM� �quantreg� �irlba� �igraph�
Do you want to attempt to install these from sources?
y/n: y
trying URL 
'https://bioconductor.org/packages/3.5/bioc/bin/macosx/mavericks/contrib/3.4/MWASTools_0.99.10.tgz'
Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
==
downloaded 2.1 MB


The downloaded binary packages are in
/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn/T//Rtmp79qF9E/downloaded_packages
installing the source packages �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==
downloaded 52 KB

trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.tar.gz'
Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
==
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
==
downloaded 3.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
Content type 'application/x-gzip' length 737540 bytes (720 KB)
==
downloaded 720 KB

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
==
downloaded 161 KB

trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
==
downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
Content type 'application/x-gzip' length 218471 bytes (213 KB)
==
downloaded 213 KB

trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
==
downloaded 608 KB

trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
==
downloaded 3.2 MB

* installing *source* package �minqa� ...
** package �minqa� successfully unpacked and MD5 sums checked
** libs
gfortran-4.8   -fPIC  -g -O2  -c altmov.f -o altmov.o
make: gfortran-4.8: No such file or directory
make: *** [altmov.o] Error 1
ERROR: compilation failed for package �minqa�
* removing 
�/Library/Frameworks/R.framework/Versions/3.4/Resources/library/minqa�
* installing *source* package �RcppEigen� ...
** package �RcppEigen� successfully unpacked and MD5 sums checked
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include 
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" 
 -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppEigen.cpp -o 
RcppEigen.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include 
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" 
 -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o 
RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include 
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" 
 -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c fastLm.cpp -o fastLm.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
-single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
RcppEigen.so RcppEigen.o RcppExports.o fastLm.o 
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack 
-L/Library/Frameworks/R.framework/Resources/lib -lRblas 
-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Kasper Daniel Hansen

You are not set up to compile from source.  Specifically, you're missing a
fortran compiler (gfortran)

On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martine...@imperial.ac.uk> wrote:

> This is all I get:
>
> > source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> > biocLite("MWASTools")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
> (unstable) (2016-10-26 r71594).
> Installing package(s) ‘MWASTools’
> also installing the dependencies ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
>   cannot download all files
> Packages which are only available in source form, and may need compilation
> of C/C++/Fortran:
>   ‘minqa’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘irlba’ ‘igraph’
> Do you want to attempt to install these from sources?
> y/n: y
> trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/
> mavericks/contrib/3.4/MWASTools_0.99.10.tgz'
> Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
> ==
> downloaded 2.1 MB
>
>
> The downloaded binary packages are in
> /var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn/T//Rtmp79qF9E/downloaded_
> packages
> installing the source packages ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
> Content type 'application/x-gzip' length 53548 bytes (52 KB)
> ==
> downloaded 52 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.
> tar.gz'
> Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
> ==
> downloaded 1.2 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
> Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
> ==
> downloaded 3.7 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
> Content type 'application/x-gzip' length 737540 bytes (720 KB)
> ==
> downloaded 720 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
> Content type 'application/x-gzip' length 165269 bytes (161 KB)
> ==
> downloaded 161 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
> Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
> Content type 'application/x-gzip' length 218471 bytes (213 KB)
> ==
> downloaded 213 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
> Content type 'application/x-gzip' length 622922 bytes (608 KB)
> ==
> downloaded 608 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
> Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
> ==
> downloaded 3.2 MB
>
> * installing *source* package ‘minqa’ ...
> ** package ‘minqa’ successfully unpacked and MD5 sums checked
> ** libs
> gfortran-4.8   -fPIC  -g -O2  -c altmov.f -o altmov.o
> make: gfortran-4.8: No such file or directory
> make: *** [altmov.o] Error 1
> ERROR: compilation failed for package ‘minqa’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/minqa’
> * installing *source* package ‘RcppEigen’ ...
> ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
> ** libs
> clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppEigen.cpp -o
> RcppEigen.o
> clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o
> RcppExports.o
> clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c fastLm.cpp -o
> fastLm.o
> clang++ -dynamiclib

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Rodriguez Martinez, Andrea

Thanks very much for the clarification.

Best wishes,

Andrea


From: Kasper Daniel Hansen 
Sent: 30 November 2016 16:26:10
To: Rodriguez Martinez, Andrea
Cc: Vincent Carey; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel 
in mac

You are not set up to compile from source.  Specifically, you're missing a 
fortran compiler (gfortran)

On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea 
>
 wrote:

This is all I get:

> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> biocLite("MWASTools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable) 
(2016-10-26 r71594).
Installing package(s) �MWASTools�
also installing the dependencies �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
  cannot download all files
Packages which are only available in source form, and may need compilation of 
C/C++/Fortran:
  �minqa� �RcppEigen� �lme4� �SparseM� �quantreg� �irlba� �igraph�
Do you want to attempt to install these from sources?
y/n: y
trying URL 
'https://bioconductor.org/packages/3.5/bioc/bin/macosx/mavericks/contrib/3.4/MWASTools_0.99.10.tgz'
Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
==
downloaded 2.1 MB


The downloaded binary packages are in
/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn/T//Rtmp79qF9E/downloaded_packages
installing the source packages �minqa�, �RcppEigen�, �lme4�, �SparseM�, 
�pbkrtest�, �quantreg�, �irlba�, �car�, �igraph�

trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==
downloaded 52 KB

trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.tar.gz'
Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
==
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
==
downloaded 3.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
Content type 'application/x-gzip' length 737540 bytes (720 KB)
==
downloaded 720 KB

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
==
downloaded 161 KB

trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
==
downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
Content type 'application/x-gzip' length 218471 bytes (213 KB)
==
downloaded 213 KB

trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
==
downloaded 608 KB

trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
==
downloaded 3.2 MB

* installing *source* package �minqa� ...
** package �minqa� successfully unpacked and MD5 sums checked
** libs
gfortran-4.8   -fPIC  -g -O2  -c altmov.f -o altmov.o
make: gfortran-4.8: No such file or directory
make: *** [altmov.o] Error 1
ERROR: compilation failed for package �minqa�
* removing 
�/Library/Frameworks/R.framework/Versions/3.4/Resources/library/minqa�
* installing *source* package �RcppEigen� ...
** package �RcppEigen� successfully unpacked and MD5 sums checked
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include 
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" 
 -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppEigen.cpp -o 
RcppEigen.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include 
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" 
 -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o 
RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include -I/usr/local/include/freetype2

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Nitesh

This should help:

https://cran.r-project.org/bin/macosx/tools/

On Wed, 30 Nov 2016 at 11:29 Rodriguez Martinez, Andrea <
andrea.rodriguez-martine...@imperial.ac.uk> wrote:

> Thanks very much for the clarification.
>
> Best wishes,
>
> Andrea
>
> 
> From: Kasper Daniel Hansen 
> Sent: 30 November 2016 16:26:10
> To: Rodriguez Martinez, Andrea
> Cc: Vincent Carey; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
> devel in mac
>
> You are not set up to compile from source.  Specifically, you're missing a
> fortran compiler (gfortran)
>
> On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea <
> andrea.rodriguez-martine...@imperial.ac.uk andrea.rodriguez-martine...@imperial.ac.uk>> wrote:
>
> This is all I get:
>
> > source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> > biocLite("MWASTools")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
> (unstable) (2016-10-26 r71594).
> Installing package(s) ‘MWASTools’
> also installing the dependencies ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
>   cannot download all files
> Packages which are only available in source form, and may need compilation
> of C/C++/Fortran:
>   ‘minqa’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘irlba’ ‘igraph’
> Do you want to attempt to install these from sources?
> y/n: y
> trying URL '
> https://bioconductor.org/packages/3.5/bioc/bin/macosx/mavericks/contrib/3.4/MWASTools_0.99.10.tgz
> '
> Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
> ==
> downloaded 2.1 MB
>
>
> The downloaded binary packages are in
>
> /var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn/T//Rtmp79qF9E/downloaded_packages
> installing the source packages ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
> Content type 'application/x-gzip' length 53548 bytes (52 KB)
> ==
> downloaded 52 KB
>
> trying URL '
> https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.tar.gz'
> Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
> ==
> downloaded 1.2 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
> Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
> ==
> downloaded 3.7 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
> Content type 'application/x-gzip' length 737540 bytes (720 KB)
> ==
> downloaded 720 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
> Content type 'application/x-gzip' length 165269 bytes (161 KB)
> ==
> downloaded 161 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
> Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
> Content type 'application/x-gzip' length 218471 bytes (213 KB)
> ==
> downloaded 213 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
> Content type 'application/x-gzip' length 622922 bytes (608 KB)
> ==
> downloaded 608 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
> Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
> ==
> downloaded 3.2 MB
>
> * installing *source* package ‘minqa’ ...
> ** package ‘minqa’ successfully unpacked and MD5 sums checked
> ** libs
> gfortran-4.8   -fPIC  -g -O2  -c altmov.f -o altmov.o
> make: gfortran-4.8: No such file or directory
> make: *** [altmov.o] Error 1
> ERROR: compilation failed for package ‘minqa’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/minqa’
> * installing *source* package ‘RcppEigen’ ...
> ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
> ** libs
> clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
> -I../inst/include -fPIC  -Wall -mtune=core2 -g -O2  -c RcppEigen.cpp -o
> RcppEigen.o
> clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG

[Bioc-devel] Error processing scater vignette Mac OS X Sierra

2016-11-30 Thread Davis McCarthy

Hi all

  

Since updating to Mac OS X Sierra (the only system change I can think of),
building the vignette in scater throws an error. It seems to be caused by
excess arguments to pandoc, but this has never been a problem until now (the
vignette hasn't changed in any major way for months).

  

Has anyone else seen this? Do you know how to fix?

  

Details (error messages, session info etc) below.

  

Best  
Davis

  

The error message reads:  
```  
Error: processing vignette 'vignette.Rmd' failed with diagnostics:  
unused arguments (self_contained, lib_dir, output_dir)  
Execution halted  
Error: Command failed (1)  
Execution halted  
  
Exited with status 1.  
```

  

Running the vignette outside of R CMD check runs fine until the final step of
converting the .md file to html, which fails with the  same error as above:

```

Error in rmarkdown:::pandoc_html_highlight_args(highlight, template =
"default",  :  
 unused arguments (self_contained, lib_dir, output_dir)  
Calls:  ->  -> overlay ->   
Execution halted  

```

  

Unfortunately there's not really enough information there for me to know
what's going on.

  

Session Info:

```

> sessionInfo()  
R version 3.3.2 (2016-10-31)  
Platform: x86_64-apple-darwin13.4.0 (64-bit)  
Running under: macOS Sierra 10.12.1  
  
locale:  
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8  
  
attached base packages:  
[1] stats graphics  grDevices utils datasets  methods   base  
  
loaded via a namespace (and not attached):  
[1] Rcpp_0.12.8  vipor_0.4.4  plyr_1.8.4
zlibbioc_1.20.0  viridis_0.3.4  
[6] bitops_1.0-6 tools_3.3.2  biomaRt_2.30.0
digest_0.6.10rhdf5_2.18.0  
[11] RSQLite_1.0.0tibble_1.2   gtable_0.2.0
lattice_0.20-34  shiny_0.14.2  
[16] DBI_0.5-1parallel_3.3.2   beeswarm_0.2.3
gridExtra_2.2.1  stringr_1.1.0  
[21] dplyr_0.5.0  scater_1.1.27S4Vectors_0.12.0
IRanges_2.8.1stats4_3.3.2  
[26] locfit_1.5-9.1   grid_3.3.2   shinydashboard_0.5.3
Biobase_2.34.0   data.table_1.9.6  
[31] R6_2.2.0 AnnotationDbi_1.36.0 XML_3.98-1.5
ggbeeswarm_0.5.0 limma_3.30.4  
[36] reshape2_1.4.2   ggplot2_2.2.0magrittr_1.5
edgeR_3.16.3 matrixStats_0.51.0  
[41] scales_0.4.1 htmltools_0.3.5  BiocGenerics_0.20.0
tximport_1.2.0   assertthat_0.1  
[46] mime_0.5 xtable_1.8-2 colorspace_1.3-1
httpuv_1.3.3 stringi_1.1.2  
[51] RCurl_1.95-4.8   lazyeval_0.2.0   munsell_0.4.3
rjson_0.2.15 chron_2.3-47  

```

  

Output of R CMD check in RStudio:

```

==> devtools::check()  
  
Updating scater documentation  
Loading scater  
Loading required package: Biobase  
Loading required package: BiocGenerics  
Loading required package: parallel  
  
Attaching package: ‘BiocGenerics’  
  
The following objects are masked from ‘package:parallel’:  
  
   clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,  
   clusterExport, clusterMap, parApply, parCapply, parLapply,  
   parLapplyLB, parRapply, parSapply, parSapplyLB  
  
The following objects are masked from ‘package:stats’:  
  
   IQR, mad, xtabs  
  
The following objects are masked from ‘package:base’:  
  
   anyDuplicated, append, as.data.frame, cbind, colnames, do.call,  
   duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,  
   is.unsorted, lapply, lengths, Map, mapply, match, mget, order,  
   paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,  
   Reduce, rownames, sapply, setdiff, sort, table, tapply, union,  
   unique, unsplit, which, which.max, which.min  
  
Welcome to Bioconductor  
  
   Vignettes contain introductory material; view with  
   'browseVignettes()'. To cite Bioconductor, see  
   'citation("Biobase")', and for packages 'citation("pkgname")'.  
  
Loading required package: ggplot2  
Creating a new generic function for ‘mutate’ in package ‘scater’  
Creating a new generic function for ‘filter’ in package ‘scater’  
Setting env vars
---  
CFLAGS  : -Wall -pedantic  
CXXFLAGS: -Wall -pedantic  
Building scater
  
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
\  
 \--no-save --no-restore --quiet CMD build  \  
 '/Users/davis/Dropbox/Projects/scater' --no-resave-data --no-manual  
  
* checking for file ‘/Users/davis/Dropbox/Projects/scater/DESCRIPTION’ ... OK  
* preparing ‘scater’:  
* checking DESCRIPTION meta-information ... OK  
* cleaning src  
* installing the package to build vignettes  
* creating vignettes ... ERROR  
  
Attaching package: 'BiocGenerics'  
  
The following objects are masked from 'package:parallel':  
  
   clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,  
   clusterExport, clusterMap, parApply, parCapply, parLapply,  
   parLapplyLB,

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

2016-11-30 Thread Obenchain, Valerie

There is a section in the vignette that describes what should be imported:

DESCRIPTION / NAMESPACE

The package should depend on and fully import ExperimentHub.
...

ExperimentHub depends on AnnotationHub. When ExperimentHub is loaded you
can see AnnotationHub attached to the search path with search().
read.csv is imported in AnnotationHub so adding this dependency should
take care of all the warnings you mentioned.

Are you depending on ExpermentHub?

Valerie

On 11/30/2016 09:52 AM, Marcin Kosiński wrote:
> Hi bioc devs!
>
> In this manual about creeating ExperimentHubData package
> http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
> there is a suggestion to create a zzz.R file where `query` function is used.
>
> This function comes from AnnotationHub package, so there somewhere someone
> should add an information about adding AnnotationHub to Imports in
> DESCRIPTION and about importing query from AnnotationHub in NAMESPACE.
> Without that the CRAN CHECK results in `query is an undocumented object or
> function`. What is more, I even had to add importFrom(utils, read.csv) to
> the NAMESPACE, just from that reason :)
>
> Cheers!
> Marcin
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Error processing scater vignette Mac OS X Sierra

2016-11-30 Thread Leonardo Collado Torres

Hi Davis,

Update your BiocStyle package to 2.2.1 (release) or 2.3.12 (devel)
which I see you are using at
https://github.com/Bioconductor-mirror/scater/blob/master/DESCRIPTION#L24.
See https://stat.ethz.ch/pipermail/bioc-devel/2016-November/010168.html
for details

Best,
Leo

On Wed, Nov 30, 2016 at 12:33 PM, Davis McCarthy  wrote:
> Hi all
>
>
>
> Since updating to Mac OS X Sierra (the only system change I can think of),
> building the vignette in scater throws an error. It seems to be caused by
> excess arguments to pandoc, but this has never been a problem until now (the
> vignette hasn't changed in any major way for months).
>
>
>
> Has anyone else seen this? Do you know how to fix?
>
>
>
> Details (error messages, session info etc) below.
>
>
>
> Best
> Davis
>
>
>
> The error message reads:
> ```
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> unused arguments (self_contained, lib_dir, output_dir)
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
> ```
>
>
>
> Running the vignette outside of R CMD check runs fine until the final step of
> converting the .md file to html, which fails with the  same error as above:
>
> ```
>
> Error in rmarkdown:::pandoc_html_highlight_args(highlight, template =
> "default",  :
>  unused arguments (self_contained, lib_dir, output_dir)
> Calls:  ->  -> overlay -> 
> Execution halted
>
> ```
>
>
>
> Unfortunately there's not really enough information there for me to know
> what's going on.
>
>
>
> Session Info:
>
> ```
>
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: macOS Sierra 10.12.1
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.8  vipor_0.4.4  plyr_1.8.4
> zlibbioc_1.20.0  viridis_0.3.4
> [6] bitops_1.0-6 tools_3.3.2  biomaRt_2.30.0
> digest_0.6.10rhdf5_2.18.0
> [11] RSQLite_1.0.0tibble_1.2   gtable_0.2.0
> lattice_0.20-34  shiny_0.14.2
> [16] DBI_0.5-1parallel_3.3.2   beeswarm_0.2.3
> gridExtra_2.2.1  stringr_1.1.0
> [21] dplyr_0.5.0  scater_1.1.27S4Vectors_0.12.0
> IRanges_2.8.1stats4_3.3.2
> [26] locfit_1.5-9.1   grid_3.3.2   shinydashboard_0.5.3
> Biobase_2.34.0   data.table_1.9.6
> [31] R6_2.2.0 AnnotationDbi_1.36.0 XML_3.98-1.5
> ggbeeswarm_0.5.0 limma_3.30.4
> [36] reshape2_1.4.2   ggplot2_2.2.0magrittr_1.5
> edgeR_3.16.3 matrixStats_0.51.0
> [41] scales_0.4.1 htmltools_0.3.5  BiocGenerics_0.20.0
> tximport_1.2.0   assertthat_0.1
> [46] mime_0.5 xtable_1.8-2 colorspace_1.3-1
> httpuv_1.3.3 stringi_1.1.2
> [51] RCurl_1.95-4.8   lazyeval_0.2.0   munsell_0.4.3
> rjson_0.2.15 chron_2.3-47
>
> ```
>
>
>
> Output of R CMD check in RStudio:
>
> ```
>
> ==> devtools::check()
>
> Updating scater documentation
> Loading scater
> Loading required package: Biobase
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
>clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>clusterExport, clusterMap, parApply, parCapply, parLapply,
>parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
>IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
>anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
>is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
>paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
>Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
>unique, unsplit, which, which.max, which.min
>
> Welcome to Bioconductor
>
>Vignettes contain introductory material; view with
>'browseVignettes()'. To cite Bioconductor, see
>'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: ggplot2
> Creating a new generic function for ‘mutate’ in package ‘scater’
> Creating a new generic function for ‘filter’ in package ‘scater’
> Setting env vars
> ---
> CFLAGS  : -Wall -pedantic
> CXXFLAGS: -Wall -pedantic
> Building scater
> 
> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
> \
>  \--no-save --no-restore --quiet CMD build  \
>  '/Users/davis/Dropbox/Projects/scater' --no-resave-data --no-manual
>
> * checking for file ‘/Users/davis/Dropbox/Projects/scater/DESCRIPTION’ ... OK
> *

[Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

2016-11-30 Thread Marcin Kosiński

Hi bioc devs!

In this manual about creeating ExperimentHubData package
http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
there is a suggestion to create a zzz.R file where `query` function is used.

This function comes from AnnotationHub package, so there somewhere someone
should add an information about adding AnnotationHub to Imports in
DESCRIPTION and about importing query from AnnotationHub in NAMESPACE.
Without that the CRAN CHECK results in `query is an undocumented object or
function`. What is more, I even had to add importFrom(utils, read.csv) to
the NAMESPACE, just from that reason :)

Cheers!
Marcin

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Sean Davis


> On Nov 30, 2016, at 4:13 PM, Martin Morgan  
> wrote:
> 
> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>> Full transcript please; you're compiling from source.
> 
> Excuse my ignorance about the Mac world but shouldn't these be available for 
> binary installation via the URL Andrea provided,
> 
>  https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/ 
> 

I am not sure if it is supposed to be, but this directory is empty.  

Sean


> 
> ?
> 
> Martin
> 
>> 
>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
>> andrea.rodriguez-martine...@imperial.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> 
>>> Thanks for your reply.  Maybe I am doing something wrong, but I do get
>>> errors, after I select the option install from source. See below:
>>> 
>>> 
 source("https://bioconductor.org/biocLite.R;)
 biocLite("MWASTools")
>>> 
>>> 
>>> The downloaded source packages are in
>>> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn
>>> /T/Rtmp79qF9E/downloaded_packages’
>>> Warning messages:
>>> 1: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘SparseM’ had non-zero exit status
>>> 2: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘irlba’ had non-zero exit status
>>> 3: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘minqa’ had non-zero exit status
>>> 4: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘RcppEigen’ had non-zero exit status
>>> 5: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘quantreg’ had non-zero exit status
>>> 6: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘lme4’ had non-zero exit status
>>> 7: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘pbkrtest’ had non-zero exit status
>>> 8: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘car’ had non-zero exit status
>>> 9: In install.packages(pkgs = doing, lib = lib, ...) :
>>>  installation of package ‘igraph’ had non-zero exit status
>>> 10: In install.packages(update[instlib == l, "Package"], l, repos =
>>> repos,  :
>>>  installation of package ‘mgcv’ had non-zero exit status
>>> 
>>> 
 sessionInfo()
>>> R Under development (unstable) (2016-10-26 r71594)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X El Capitan 10.11.6
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods   base
>>> 
>>> other attached packages:
>>> [1] BiocInstaller_1.25.2
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.4.0
>>> 
>>> 
>>> 
>>> Thanks very much in advance,
>>> 
>>> 
>>> Best wishes,
>>> 
>>> 
>>> Andrea
>>> 
>>> 
>>> From: Vincent Carey 
>>> Sent: 30 November 2016 12:39:12
>>> To: Rodriguez Martinez, Andrea
>>> Cc: bioc-devel@r-project.org
>>> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
>>> devel in mac
>>> 
>>> In fact there was a problem installing igraph from source, but that is
>>> another issue.  That can
>>> be resolved using the precompiled binary at http://igraph.org/r/#downloads
>>> 
>>> 
 sessionInfo()
>>> 
>>> R Under development (unstable) (2016-10-26 r71594)
>>> 
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> 
>>> Running under: OS X El Capitan 10.11.6
>>> 
>>> 
>>> locale:
>>> 
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> 
>>> attached base packages:
>>> 
>>> [1] stats graphics  grDevices utils datasets  methods   base
>>> 
>>> 
>>> other attached packages:
>>> 
>>> [1] BiocInstaller_1.25.2 MWASTools_0.99.10rmarkdown_1.1
>>> 
>>> 
>>> loaded via a namespace (and not attached):
>>> 
>>> [1] Rcpp_0.12.8XVector_0.15.0
>>> 
>>> [3] GenomeInfoDb_1.11.6nloptr_1.0.4
>>> 
>>> [5] ppcor_1.1  plyr_1.8.4
>>> 
>>> [7] zlibbioc_1.21.0tools_3.4.0
>>> 
>>> [9] boot_1.3-18digest_0.6.10
>>> 
>>> [11] lme4_1.1-12evaluate_0.10
>>> 
>>> [13] tibble_1.2 gtable_0.2.0
>>> 
>>> [15] nlme_3.1-128   lattice_0.20-34
>>> 
>>> [17] mgcv_1.8-16Matrix_1.2-7.1
>>> 
>>> [19] igraph_1.0.1   parallel_3.4.0
>>> 
>>> [21] SparseM_1.74   gridExtra_2.2.1
>>> 
>>> [23] stringr_1.1.0  IRanges_2.9.8
>>> 
>>> [25] S4Vectors_0.13.2   MatrixModels_0.4-1
>>> 
>>> [27] stats4_3.4.0   grid_3.4.0
>>> 
>>> [29] nnet_7.3-12Biobase_2.35.0
>>> 
>>> [31] qvalue_2.7.0   minqa_1.2.4
>>> 
>>> [33] ggplot2_2.2.0  reshape2_1.4.2
>>> 
>>> [35] car_2.1-3  glm2_1.1.2

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Martin Morgan


On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:

Full transcript please; you're compiling from source.


Excuse my ignorance about the Mac world but shouldn't these be available 
for binary installation via the URL Andrea provided,


  https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/

?

Martin



On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martine...@imperial.ac.uk> wrote:


Hi,


Thanks for your reply.  Maybe I am doing something wrong, but I do get
errors, after I select the option install from source. See below:



source("https://bioconductor.org/biocLite.R;)
biocLite("MWASTools")



The downloaded source packages are in
‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn
/T/Rtmp79qF9E/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SparseM’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘irlba’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘minqa’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppEigen’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘quantreg’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘lme4’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘pbkrtest’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘car’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘igraph’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, repos =
repos,  :
  installation of package ‘mgcv’ had non-zero exit status



sessionInfo()

R Under development (unstable) (2016-10-26 r71594)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.25.2

loaded via a namespace (and not attached):
[1] tools_3.4.0



Thanks very much in advance,


Best wishes,


Andrea


From: Vincent Carey 
Sent: 30 November 2016 12:39:12
To: Rodriguez Martinez, Andrea
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
devel in mac

In fact there was a problem installing igraph from source, but that is
another issue.  That can
be resolved using the precompiled binary at http://igraph.org/r/#downloads



sessionInfo()


R Under development (unstable) (2016-10-26 r71594)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X El Capitan 10.11.6


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] BiocInstaller_1.25.2 MWASTools_0.99.10rmarkdown_1.1


loaded via a namespace (and not attached):

 [1] Rcpp_0.12.8XVector_0.15.0

 [3] GenomeInfoDb_1.11.6nloptr_1.0.4

 [5] ppcor_1.1  plyr_1.8.4

 [7] zlibbioc_1.21.0tools_3.4.0

 [9] boot_1.3-18digest_0.6.10

[11] lme4_1.1-12evaluate_0.10

[13] tibble_1.2 gtable_0.2.0

[15] nlme_3.1-128   lattice_0.20-34

[17] mgcv_1.8-16Matrix_1.2-7.1

[19] igraph_1.0.1   parallel_3.4.0

[21] SparseM_1.74   gridExtra_2.2.1

[23] stringr_1.1.0  IRanges_2.9.8

[25] S4Vectors_0.13.2   MatrixModels_0.4-1

[27] stats4_3.4.0   grid_3.4.0

[29] nnet_7.3-12Biobase_2.35.0

[31] qvalue_2.7.0   minqa_1.2.4

[33] ggplot2_2.2.0  reshape2_1.4.2

[35] car_2.1-3  glm2_1.1.2

[37] magrittr_1.5   GenomicRanges_1.27.12

[39] scales_0.4.1   htmltools_0.3.5

[41] MASS_7.3-45splines_3.4.0

[43] BiocGenerics_0.21.0assertthat_0.1

[45] pbkrtest_0.4-6 SummarizedExperiment_1.5.3

[47] colorspace_1.3-1   quantreg_5.29

[49] stringi_1.1.2  lazyeval_0.2.0

[51] munsell_0.4.3

On Wed, Nov 30, 2016 at 7:27 AM, Vincent Carey > wrote:
sessionInfo()?  I just did biocLite("MWASTools") with a devel version of
R/BiocInstaller,
and it seems to work well.

On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martine...@imperial.ac.uk> wrote:
Hi,


I'm trying to

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Dan Tenenbaum



- Original Message -
> From: "Sean Davis" 
> To: "Martin Morgan" 
> Cc: "bioc-devel" 
> Sent: Wednesday, November 30, 2016 1:20:58 PM
> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC 
> devel in mac

>> On Nov 30, 2016, at 4:13 PM, Martin Morgan 
>> wrote:
>> 
>> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>>> Full transcript please; you're compiling from source.
>> 
>> Excuse my ignorance about the Mac world but shouldn't these be available for
>> binary installation via the URL Andrea provided,
>> 
>>  https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>>  
> 
> I am not sure if it is supposed to be, but this directory is empty.
> 

Building binaries of packages for R-devel is not always CRAN's highest 
priority, but it could be worth asking about. Simon Urbanek is the Mac person 
at CRAN.

Dan


> Sean
> 
> 
>> 
>> ?
>> 
>> Martin
>> 
>>> 
>>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
>>> andrea.rodriguez-martine...@imperial.ac.uk> wrote:
>>> 
 Hi,
 
 
 Thanks for your reply.  Maybe I am doing something wrong, but I do get
 errors, after I select the option install from source. See below:
 
 
> source("https://bioconductor.org/biocLite.R;)
> biocLite("MWASTools")
 
 
 The downloaded source packages are in
 ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn
 /T/Rtmp79qF9E/downloaded_packages’
 Warning messages:
 1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SparseM’ had non-zero exit status
 2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘irlba’ had non-zero exit status
 3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘minqa’ had non-zero exit status
 4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppEigen’ had non-zero exit status
 5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘quantreg’ had non-zero exit status
 6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘lme4’ had non-zero exit status
 7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘pbkrtest’ had non-zero exit status
 8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘car’ had non-zero exit status
 9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘igraph’ had non-zero exit status
 10: In install.packages(update[instlib == l, "Package"], l, repos =
 repos,  :
  installation of package ‘mgcv’ had non-zero exit status
 
 
> sessionInfo()
 R Under development (unstable) (2016-10-26 r71594)
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 Running under: OS X El Capitan 10.11.6
 
 locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 
 other attached packages:
 [1] BiocInstaller_1.25.2
 
 loaded via a namespace (and not attached):
 [1] tools_3.4.0
 
 
 
 Thanks very much in advance,
 
 
 Best wishes,
 
 
 Andrea
 
 
 From: Vincent Carey 
 Sent: 30 November 2016 12:39:12
 To: Rodriguez Martinez, Andrea
 Cc: bioc-devel@r-project.org
 Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
 devel in mac
 
 In fact there was a problem installing igraph from source, but that is
 another issue.  That can
 be resolved using the precompiled binary at http://igraph.org/r/#downloads
 
 
> sessionInfo()
 
 R Under development (unstable) (2016-10-26 r71594)
 
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 
 Running under: OS X El Capitan 10.11.6
 
 
 locale:
 
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
 
 attached base packages:
 
 [1] stats graphics  grDevices utils datasets  methods   base
 
 
 other attached packages:
 
 [1] BiocInstaller_1.25.2 MWASTools_0.99.10rmarkdown_1.1
 
 
 loaded via a namespace (and not attached):
 
 [1] Rcpp_0.12.8XVector_0.15.0
 
 [3] GenomeInfoDb_1.11.6nloptr_1.0.4
 
 [5] ppcor_1.1  plyr_1.8.4
 
 [7] zlibbioc_1.21.0tools_3.4.0
 
 [9] boot_1.3-18digest_0.6.10
 
 [11] lme4_1.1-12evaluate_0.10
 
 [13] tibble_1.2

[Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Rodriguez Martinez, Andrea

Hi,


I'm trying to install my MWASTools package (devel branch) in mac, and I get a 
lot of errors regarding the installation of the dependencies from CRAN because 
there are no files in the repository:

https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/


For windows, I dont have any problems with the installation because the cran 
repository has the files:

https://cran.rstudio.com/bin/windows/contrib/r-devel/


One solution, is to install the CRAN dependencies in advance using

>install.packages(pkgs, contriburl = 
>"https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.3/;)


I wonder if there is another solution to do this directly from biocLite.


Thanks very much,


Andrea






[[alternative HTML version deleted]]

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Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

2016-11-30 Thread Vincent Carey

sessionInfo()?  I just did biocLite("MWASTools") with a devel version of
R/BiocInstaller,
and it seems to work well.

On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martine...@imperial.ac.uk> wrote:

> Hi,
>
>
> I'm trying to install my MWASTools package (devel branch) in mac, and I
> get a lot of errors regarding the installation of the dependencies from
> CRAN because there are no files in the repository:
>
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>
>
> For windows, I dont have any problems with the installation because the
> cran repository has the files:
>
> https://cran.rstudio.com/bin/windows/contrib/r-devel/
>
>
> One solution, is to install the CRAN dependencies in advance using
>
> >install.packages(pkgs, contriburl = "https://cran.rstudio.com/bin/
> macosx/mavericks/contrib/3.3/")
>
>
> I wonder if there is another solution to do this directly from biocLite.
>
>
> Thanks very much,
>
>
> Andrea
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

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Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

[Bioc-devel] problems installing cran dependencies with BioC devel in mac

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

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