![Tcl/tk download mac software Tcl/tk download mac software](/uploads/1/1/9/3/119381951/689085247.png)
Background
Sometimes data is very skewed and contains a lot of ‘zeros’ (or very small numbers approaching ‘zero’). Before analyses such data need normalisation to meet the assumptions of a statistical test (you can find more on transformation and normalisation here). Usually people log-transform (e.g. natural log, or log2), the disadvantage is that you loose the ‘zeros’.
In my case that is an issue, because the measurements made were properly done (no technical issues), so ‘zero’ really represents ‘zero’. In other words: I don’t want to loose them. Some years back a colleague of mine pointed me to *‘Box-Cox’ transformation** (you can find more on that here), and this method is available in
R
via the geoR
package. Hence, the reason for this post.- This page describes how to obtain a Tcl/Tk source release. See Binary distributions for obtaining pre-built binaries. The main site for Tcl/Tk source distributions is SourceForge. The files are also available from ftp.tcl.tk or one of its mirrors. The latest downloads for the Tcl 8.6 and 8.7 release sequences are shown in the table below.
- If you omitted that build directive, then home brew will compile the Python version to use Apple's default Tcl/Tk 8.5.9. If you download Python dot org's Python binary, either before, or after you install ActiveState 8.5.18 Tcl/Tk libraries, it will use these libraries because that is what Python dot org compiles its binary distribution to use.
The Python for Mac OS X installers downloaded from this website dynamically link at runtime to Tcl/Tk Mac OS X frameworks. The Tcl/Tk major version is determined when the installer is created and cannot be overridden. The Python 64-bit/32-bit Mac OS X installers for Python 3.4.x, 3.3.x, 3.2.x, and 2.7.x dynamically link to Tcl/Tk 8.5 frameworks.
The thing is: I use
brew
to install R
and many other packages/libraries lacking on macOS, e.g.wget
. For reasons I still don’t get - but I also realize it’s beyond my coding capabilities - brew
does not normally install R
with the tcl-tk
package. And let that be the critical part you need for geoR
and by extension the function boxccoxfit
to work. After some googling I got some hints that led me to a (on the face of it) permanent solution; the discussion on the brew
website were critical.Step-by-step
- I made sure I have tcl-tk installed via
brew
.brew install tcl-tk
- I made sure
tcl-tk
was in my path:echo 'export PATH='/usr/local/opt/tcl-tk/bin:$PATH' >> ~/.bash_profile
. - The command
wish
also confirmed this.
- I also made sure I had installed Command Line Tools properly - there were some updates to High Sierra in the last week, and based on the discussions above I feared it might had to re-installed. I didn’t have to, but here’s how I checked that. The command
brew config
shows:
HOMEBREW_VERSION: 1.5.2
ORIGIN: https://github.com/Homebrew/brew
HEAD: 60a30e966b7cece5bd4823dae3fb981ab85106ea
Last commit: 13 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 8c1c4f86a269cb23d9d92008abf1a37eabb297b6
Core tap last commit: 2 days ago
HOMEBREW_PREFIX: /usr/local
CPU: quad-core 64-bit skylake
Homebrew Ruby: 2.3.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 9.0 build 900
Git: 2.16.1 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /usr/local/opt/python/libexec/bin/python => /usr/local/Cellar/python/2.7.14_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Java: 9.0.1
macOS: 10.13.3-x86_64
Xcode: N/A
** CLT: 9.2.0.0.1.1510905681**
X11: 2.7.11 => /opt/X11
ORIGIN: https://github.com/Homebrew/brew
HEAD: 60a30e966b7cece5bd4823dae3fb981ab85106ea
Last commit: 13 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 8c1c4f86a269cb23d9d92008abf1a37eabb297b6
Core tap last commit: 2 days ago
HOMEBREW_PREFIX: /usr/local
CPU: quad-core 64-bit skylake
Homebrew Ruby: 2.3.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 9.0 build 900
Git: 2.16.1 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /usr/local/opt/python/libexec/bin/python => /usr/local/Cellar/python/2.7.14_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Java: 9.0.1
macOS: 10.13.3-x86_64
Xcode: N/A
** CLT: 9.2.0.0.1.1510905681**
X11: 2.7.11 => /opt/X11
The bold printed line suggests that
3. I than double checked if the path was really set, using the command
Command Line Tools
should be installed.3. I than double checked if the path was really set, using the command
xcode-select -p
, which shows:/Library/Developer/CommandLineTools
4. Also
gcc
is properly set. I checked this using gcc --version
, which shows:Configured with: –prefix=/Library/Developer/CommandLineTools/usr –with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
5. Now that I had confirmed the basics are present, I proceeded by re-installing
Xquartz
, R
and RStudio
. To make sure I get the R
withtcl-tk
I used the R version of @srfore. These are the subsequent commands.brew cask install xquartz
, installXquartz
. Although some suggested this should not be necessary.brew install -s sethrfore/homebrew-r-srf/r
, installed an edited version ofR
.brew cask install rstudio
, installRstudio
.
6. All seemed well, I double checked with
brew doctor
.Your system is ready to brew.
Tcl Tk 8.6
7. Of course, for me, this all started with the need to use the function
boxcoxfit
from the R
package geoR
which is dependent on tcl-tk
. So, now it was showtime and I started R:install.packages(“geoR”)
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
— Please select a CRAN mirror for use in this session --
Secure CRAN mirrors
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
— Please select a CRAN mirror for use in this session --
Secure CRAN mirrors
1: 0-Cloud [https] 2: Algeria [https]
3: Australia (Canberra) [https] 4: Australia (Melbourne 1) [https]
5: Australia (Melbourne 2) [https] 6: Australia (Perth) [https]
7: Austria [https] 8: Belgium (Ghent) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https]
11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Chile 1 [https]
15: Chile 2 [https] 16: China (Guangzhou) [https]
17: China (Lanzhou) [https] 18: China (Shanghai) [https]
19: Colombia (Cali) [https] 20: Czech Republic [https]
21: Denmark [https] 22: East Asia [https]
23: Ecuador (Cuenca) [https] 24: Estonia [https]
25: France (Lyon 1) [https] 26: France (Lyon 2) [https]
27: France (Marseille) [https] 28: France (Montpellier) [https]
29: France (Paris 2) [https] 30: Germany (Erlangen) [https]
31: Germany (Göttingen) [https] 32: Germany (Münster) [https]
33: Greece [https] 34: Iceland [https]
35: Indonesia (Jakarta) [https] 36: Ireland [https]
37: Italy (Padua) [https] 38: Japan (Tokyo) [https]
39: Japan (Yonezawa) [https] 40: Malaysia [https]
41: Mexico (Mexico City) [https] 42: Norway [https]
43: Philippines [https] 44: Serbia [https]
45: Spain (A Coruña) [https] 46: Spain (Madrid) [https]
47: Sweden [https] 48: Switzerland [https]
49: Turkey (Denizli) [https] 50: Turkey (Mersin) [https]
51: UK (Bristol) [https] 52: UK (Cambridge) [https]
53: UK (London 1) [https] 54: USA (CA 1) [https]
55: USA (IA) [https] 56: USA (KS) [https]
57: USA (MI 1) [https] 58: USA (NY) [https]
59: USA (OR) [https] 60: USA (TN) [https]
61: USA (TX 1) [https] 62: Vietnam [https]
63: (other mirrors)
3: Australia (Canberra) [https] 4: Australia (Melbourne 1) [https]
5: Australia (Melbourne 2) [https] 6: Australia (Perth) [https]
7: Austria [https] 8: Belgium (Ghent) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https]
11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Chile 1 [https]
15: Chile 2 [https] 16: China (Guangzhou) [https]
17: China (Lanzhou) [https] 18: China (Shanghai) [https]
19: Colombia (Cali) [https] 20: Czech Republic [https]
21: Denmark [https] 22: East Asia [https]
23: Ecuador (Cuenca) [https] 24: Estonia [https]
25: France (Lyon 1) [https] 26: France (Lyon 2) [https]
27: France (Marseille) [https] 28: France (Montpellier) [https]
29: France (Paris 2) [https] 30: Germany (Erlangen) [https]
31: Germany (Göttingen) [https] 32: Germany (Münster) [https]
33: Greece [https] 34: Iceland [https]
35: Indonesia (Jakarta) [https] 36: Ireland [https]
37: Italy (Padua) [https] 38: Japan (Tokyo) [https]
39: Japan (Yonezawa) [https] 40: Malaysia [https]
41: Mexico (Mexico City) [https] 42: Norway [https]
43: Philippines [https] 44: Serbia [https]
45: Spain (A Coruña) [https] 46: Spain (Madrid) [https]
47: Sweden [https] 48: Switzerland [https]
49: Turkey (Denizli) [https] 50: Turkey (Mersin) [https]
51: UK (Bristol) [https] 52: UK (Cambridge) [https]
53: UK (London 1) [https] 54: USA (CA 1) [https]
55: USA (IA) [https] 56: USA (KS) [https]
57: USA (MI 1) [https] 58: USA (NY) [https]
59: USA (OR) [https] 60: USA (TN) [https]
61: USA (TX 1) [https] 62: Vietnam [https]
63: (other mirrors)
Selection: 1
trying URL ‘https://cloud.r-project.org/src/contrib/geoR_1.7-5.2.tar.gz'
Content type ‘application/x-gzip’ length 421612 bytes (411 KB)
downloaded 411 KB
trying URL ‘https://cloud.r-project.org/src/contrib/geoR_1.7-5.2.tar.gz'
Content type ‘application/x-gzip’ length 421612 bytes (411 KB)
downloaded 411 KB
![Tcl tk download mac software Tcl tk download mac software](/uploads/1/1/9/3/119381951/434308427.jpg)
* installing source package ‘geoR’ …
** package ‘geoR’ successfully unpacked and MD5 sums checked
** libs
clang -I/usr/local/Cellar/r/3.4.3_1/lib/R/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c geoR.c -o geoR.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.4.3_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o geoR.so geoR.o -L/usr/local/Cellar/r/3.4.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.4/site-library/geoR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (geoR)
The downloaded source packages are in
‘/private/var/folders/kh/0s66cjl5487fg_fhwgxqd2340000gn/T/RtmpHJHtGf/downloaded_packages’
** package ‘geoR’ successfully unpacked and MD5 sums checked
** libs
clang -I/usr/local/Cellar/r/3.4.3_1/lib/R/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c geoR.c -o geoR.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.4.3_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o geoR.so geoR.o -L/usr/local/Cellar/r/3.4.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.4/site-library/geoR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (geoR)
The downloaded source packages are in
‘/private/var/folders/kh/0s66cjl5487fg_fhwgxqd2340000gn/T/RtmpHJHtGf/downloaded_packages’
And loading
geoR
was not an issue:library(“geoR”)
————————————————————–
Analysis of Geostatistical Data
For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
geoR version 1.7-5.2 (built on 2016-05-02) is now loaded
————————————————————–
————————————————————–
Analysis of Geostatistical Data
For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
geoR version 1.7-5.2 (built on 2016-05-02) is now loaded
————————————————————–
So, finally, I have
boxcoxfit()
available. I’m all set to normalise my data using Box-Cox
transformations.Tcl/tk Download Mac Download
Tcl Tk
© Copyright. 1979-2018 Sander W. van der Laan. Released under the MIT license.