I don't know what goes wrong or how to fix it. Can you please help me with this?
> install.packages("TSclust")
% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 342k 100 342k 0 0 394k 0 --:--:-- --:--:-- --:--:-- 394k
The downloaded binary packages are in
/var/folders/bk/2b2d879912bgnl5s768s7crh0000gn/T//RtmpHpu6uh/downloaded_packages
> require(TSclust)
Loading required package: TSclust
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /usr/X11/lib/libGLU.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/rgl/libs/rgl.so
Reason: image not found
>
Here's info about my RStudio:
Version 0.99.473 – © 2009-2015 RStudio, Inc.
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/600.8.9 (KHTML, like Gecko)
And R:
dyn-72-33-222-106:~ mona$ R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
UPDATE:
> install.packages("TSclust")
also installing the dependencies ‘splus2R’, ‘ifultools’, ‘proxy’, ‘clv’, ‘rgl’, ‘misc3d’, ‘wmtsa’, ‘pdc’, ‘locpol’, ‘dtw’, ‘longitudinalData’
There are binary versions available but the source versions are later:
binary source needs_compilation
rgl 0.95.1201 0.95.1337 TRUE
longitudinalData 2.3 2.4 FALSE
Do you want to install from sources the package which needs compilation?
y/n: y
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/splus2R_1.2-0.tgz'
Content type 'application/x-gzip' length 190385 bytes (185 KB)
==================================================
downloaded 185 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/ifultools_2.0-1.tgz'
Content type 'application/x-gzip' length 961357 bytes (938 KB)
==================================================
downloaded 938 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/proxy_0.4-15.tgz'
Content type 'application/x-gzip' length 142040 bytes (138 KB)
==================================================
downloaded 138 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/clv_0.3-2.1.tgz'
Content type 'application/x-gzip' length 166056 bytes (162 KB)
==================================================
downloaded 162 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/misc3d_0.8-4.tgz'
Content type 'application/x-gzip' length 151783 bytes (148 KB)
==================================================
downloaded 148 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/wmtsa_2.0-0.tgz'
Content type 'application/x-gzip' length 361400 bytes (352 KB)
==================================================
downloaded 352 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/pdc_1.0.2.tgz'
Content type 'application/x-gzip' length 168385 bytes (164 KB)
==================================================
downloaded 164 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/locpol_0.6-0.tgz'
Content type 'application/x-gzip' length 104555 bytes (102 KB)
==================================================
downloaded 102 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/dtw_1.18-1.tgz'
Content type 'application/x-gzip' length 737519 bytes (720 KB)
==================================================
downloaded 720 KB
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/TSclust_1.2.3.tgz'
Content type 'application/x-gzip' length 353039 bytes (344 KB)
==================================================
downloaded 344 KB
The downloaded binary packages are in
/var/folders/bk/2b2d879912bgnl5s768s7crh0000gn/T//Rtmp258LNe/downloaded_packages
installing the source packages ‘rgl’, ‘longitudinalData’
trying URL 'https://cran.rstudio.com/src/contrib/rgl_0.95.1337.tar.gz'
Content type 'application/x-gzip' length 2189241 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/longitudinalData_2.4.tar.gz'
Content type 'application/x-gzip' length 80334 bytes (78 KB)
==================================================
downloaded 78 KB
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for gcc... (cached) clang
checking whether we are using the GNU C compiler... (cached) yes
checking whether clang accepts -g... (cached) yes
checking for clang option to accept ISO C89... (cached) none needed
checking whether __attribute__((visibility())) is supported... no
checking whether clang accepts -fvisibility... yes
checking whether accepts -fvisibility... no
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
ERROR: dependency ‘rgl’ is not available for package ‘longitudinalData’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/longitudinalData’
Warning in install.packages :
installation of package ‘longitudinalData’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/bk/2b2d879912bgnl5s768s7crh0000gn/T/Rtmp258LNe/downloaded_packages’
> require(TSclust)
Loading required package: TSclust
Loading required package: wmtsa
Loading required package: splus2R
Loading required package: ifultools
Loading required package: MASS
Loading required package: pdc
Loading required package: cluster
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘longitudinalData’
> set.seed(12349)
> n = 100
> x <- rnorm(n) #generate sample series, white noise and a wiener process
> y <- cumsum(rnorm(n))
> w <- 20 #amount of equal-sized frames to divide the series, parameters for PAA
> alpha <- 4 #size of the alphabet, parameter for SAX
> #normalize
> x <- (x - mean(x)) /sd(x)
> y <- (y - mean(y)) /sd(y)
> paax <- PAA(x, w) #generate PAA reductions
Error: could not find function "PAA"
And rgl:
> library(rgl)
Error in library(rgl) : there is no package called ‘rgl’
> install.packages("rgl")
There is a binary version available but the source version is later:
binary source needs_compilation
rgl 0.95.1201 0.95.1337 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘rgl’
trying URL 'https://cran.rstudio.com/src/contrib/rgl_0.95.1337.tar.gz'
Content type 'application/x-gzip' length 2189241 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for gcc... (cached) clang
checking whether we are using the GNU C compiler... (cached) yes
checking whether clang accepts -g... (cached) yes
checking for clang option to accept ISO C89... (cached) none needed
checking whether __attribute__((visibility())) is supported... no
checking whether clang accepts -fvisibility... yes
checking whether accepts -fvisibility... no
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/bk/2b2d879912bgnl5s768s7crh0000gn/T/Rtmp258LNe/downloaded_packages’
This means you failed to install Xquartz. It’s not an R package. You need to download from its website and install from its installer pkg. It’s an equivalent of X11 on the Mac. ALWAYS update quartz anytime you update R.
In your situation you might get away with install the ‘rgl’ pkg from binary image.