R Sig Mac Problem Loading Tcl Tk Interface On R For Mac



Background

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Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac.

  • R tcl/tk package running Mac OS X not working. Tcltk Loading Tcl/Tk interface. Done a1s breaks wool tension 1 26 A L 2 30 A L 3 54 A L 4 25 A L 5 70 A L 6 52.
  • Tcl is not the fastest in heavy number-crunching, as needed when going over many thousands of pixels, but I wouldn't consider C for a fun project;) So take your time, or get a real CPU. At least you can watch the progress, as the target image is updated after every row. Edge enhancement by Laplace5 filter.
  • Configure RpgSQL on Mac. Configuration to make RpgSQL work might be not needed for other platforms, but in my Mac box with Mac OSX 10.5 it is needed. Make sure postgresql-jdbc port is installed, or sudo port instal postgresql-jdbc. Change jar file name. Without changing the jar file name, RpgSQL is unable to locate the jar file automatically.

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.

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 Rwith 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

  1. 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.
  2. 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

The bold printed line suggests that 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


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 Rwithtcl-tk I used the R version of @srfore. These are the subsequent commands.

  • brew cask install xquartz, install Xquartz. Although some suggested this should not be necessary.
  • brew install -s sethrfore/homebrew-r-srf/r, installed an edited version of R.
  • brew cask install rstudio, install Rstudio.


6. All seemed well, I double checked with brew doctor.

Your system is ready to brew.


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

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)

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

* 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’


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
————————————————————–

So, finally, I have boxcoxfit() available. I’m all set to normalise my data using Box-Cox transformations.

R Sig Mac Problem Loading Tcl Tk Interface On R For Mac Os


R Sig Mac Problem Loading Tcl Tk Interface On R For Mac Osx

© Copyright. 1979-2018 Sander W. van der Laan. Released under the MIT license.