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Welcome to Open Source World, BAby!

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wac14004 committed Oct 17, 2015
0 parents commit 005c1b1ecadce05a8ea2b2f3699c3053564a1e44
Showing 2,469 changed files with 516,294 additions and 0 deletions.
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# sometimes I temporarily install some packages to ~/R-tmp; normall I install to ~/R
R_LIBS_USER="~/R:~/R-tmp:~/R-bioc"

# custom knitr options for me
R_KNITR_OPTIONS="knitr.chunk.tidy=TRUE"

#_R_CHECK_CRAN_INCOMING_=FALSE
# do not force installing packages in Suggests
_R_CHECK_FORCE_SUGGESTS_=false

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options(
repos = c(CRAN = 'https://cran.rstudio.com'),
help_type = 'text', width = 80, github.user = 'yihui', shiny.reactlog = TRUE,
devtools.name = 'Yihui Xie', devtools.desc.author = 'Yihui Xie <xie@yihui.name>',
devtools.desc.license = 'GPL',
warnPartialMatchAttr = TRUE, warnPartialMatchDollar = TRUE
)

if (.Platform$OS.type == 'unix') {
options(browser = 'google-chrome')
}

if (interactive()) {
d = list(
h = function(pkg) help(package = (pkg), help_type = 'html'),
i = function(...) devtools::install_github(...),
r = function() {
d1 = grep('^/usr/', .libPaths(), value = TRUE)
d2 = setdiff(.libPaths(), d1)
p1 = .packages(TRUE, d1)
p2 = .packages(TRUE, d2)
for (i in intersect(p1, p2)) {
message('Removing ', i)
remove.packages(i)
}
}
)
}
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alias R='R --no-save -q'
alias sasdesk='rdesktop -u xie -d IASTATE sas.stat.iastate.edu'
alias Rbatch='R CMD BATCH --no-restore --no-save --no-timing'
alias aptup='sudo apt-get update; sudo apt-get upgrade'
alias aptrm='sudo apt-get autoremove; sudo apt-get autoclean'

@@ -0,0 +1,2 @@
GREP_OPTIONS="--exclude-dir=\.svn --exclude-dir=\.Rproj\.user --exclude-dir=\.git"
export GREP_OPTIONS
@@ -0,0 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<buildpath>
<buildpathentry kind="src" path="src"/>
<buildpathentry kind="con" path="org.eclipse.dltk.launching.INTERPRETER_CONTAINER"/>
</buildpath>
221 .cproject
@@ -0,0 +1,221 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?fileVersion 4.0.0?>

<cproject>
<storageModule moduleId="org.eclipse.cdt.core.settings">
<cconfiguration id="preference.org.eclipse.cdt.managedbuilder.core.configurationDataProvider.1510318341">
<storageModule moduleId="cdtBuildSystem" version="4.0.0">
<configuration artifactName="luci" buildProperties="" description="" id="preference.org.eclipse.cdt.managedbuilder.core.configurationDataProvider.1510318341" name="Preference Configuration" parent="org.eclipse.cdt.build.core.prefbase.cfg">
<folderInfo id="preference.org.eclipse.cdt.managedbuilder.core.configurationDataProvider.1510318341." name="/" resourcePath="">
<toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.407447051" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain">
<targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.407447051.1470931541" name=""/>
<builder id="org.eclipse.cdt.build.core.settings.default.builder.823611263" keepEnvironmentInBuildfile="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/>
<tool id="org.eclipse.cdt.build.core.settings.holder.libs.1685234798" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/>
<tool id="org.eclipse.cdt.build.core.settings.holder.570824141" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder">
<option id="org.eclipse.cdt.build.core.settings.holder.incpaths.491129717" name="Include Paths" superClass="org.eclipse.cdt.build.core.settings.holder.incpaths" valueType="includePath">
<listOptionValue builtIn="false" value="/usr/include/lua5.1"/>
<listOptionValue builtIn="false" value="/usr/include"/>
</option>
<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.858094059" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
</tool>
<tool id="org.eclipse.cdt.build.core.settings.holder.344617955" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder">
<option id="org.eclipse.cdt.build.core.settings.holder.incpaths.564526987" name="Include Paths" superClass="org.eclipse.cdt.build.core.settings.holder.incpaths" valueType="includePath">
<listOptionValue builtIn="false" value="/usr/include/lua5.1"/>
<listOptionValue builtIn="false" value="/usr/include"/>
</option>
<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1426860237" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
</tool>
<tool id="org.eclipse.cdt.build.core.settings.holder.869454750" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder">
<option id="org.eclipse.cdt.build.core.settings.holder.incpaths.838425449" name="Include Paths" superClass="org.eclipse.cdt.build.core.settings.holder.incpaths" valueType="includePath">
<listOptionValue builtIn="false" value="/usr/include/lua5.1"/>
<listOptionValue builtIn="false" value="/usr/include"/>
</option>
<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1755775295" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
</tool>
</toolChain>
</folderInfo>
</configuration>
</storageModule>
<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="preference.org.eclipse.cdt.managedbuilder.core.configurationDataProvider.1510318341" moduleId="org.eclipse.cdt.core.settings" name="Preference Configuration">
<externalSettings/>
<extensions>
<extension id="org.eclipse.cdt.core.VCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
<extension id="org.eclipse.cdt.core.MakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
</extensions>
</storageModule>
<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
<storageModule moduleId="scannerConfiguration">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="makefileGenerator">
<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<scannerConfigBuildInfo instanceId="preference.org.eclipse.cdt.managedbuilder.core.configurationDataProvider.1510318341">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="makefileGenerator">
<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
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<buildOutputProvider>
<openAction enabled="true" filePath=""/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
<parser enabled="true"/>
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<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
<parser enabled="true"/>
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</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
<parser enabled="true"/>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
<buildOutputProvider>
<openAction enabled="true" filePath=""/>
<parser enabled="true"/>
</buildOutputProvider>
<scannerInfoProvider id="specsFile">
<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
<parser enabled="true"/>
</scannerInfoProvider>
</profile>
</scannerConfigBuildInfo>
</storageModule>
</cconfiguration>
</storageModule>
<storageModule moduleId="cdtBuildSystem" version="4.0.0">
<project id="luci.null.949486034" name="luci"/>
</storageModule>
</cproject>
47 .emacs
@@ -0,0 +1,47 @@
(custom-set-variables
;; custom-set-variables was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(column-number-mode t)
'(ess-ask-for-ess-directory nil)
'(ess-history-file nil)
'(ess-language "R")
'(ess-roxy-template-alist (list (cons "description" "") (cons "details" "") (cons "param" "") (cons "return" "") (cons "author" "Yihui Xie <\\url{http://yihui.name}>") (cons "examples" "")))
'(ess-user-full-name "Yihui Xie <\\url{http://yihui.name}>")
'(inferior-R-args "--no-save")
'(inferior-R-program-name "R")
'(inhibit-startup-screen t)
'(make-backup-files nil)
'(scroll-bar-mode (quote right))
'(x-select-enable-clipboard t))
;;; ESS
(add-hook 'ess-mode-hook
(lambda ()
(ess-set-style 'C++ 'quiet)
;; Because
;; DEF GNU BSD K&R C++
;; ess-indent-level 2 2 8 5 4
;; ess-continued-statement-offset 2 2 8 5 4
;; ess-brace-offset 0 0 -8 -5 -4
;; ess-arg-function-offset 2 4 0 0 0
;; ess-expression-offset 4 2 8 5 4
;; ess-else-offset 0 0 0 0 0
;; ess-close-brace-offset 0 0 0 0 0
(add-hook 'local-write-file-hooks
(lambda ()
(ess-nuke-trailing-whitespace)))))
;; (setq ess-nuke-trailing-whitespace-p 'ask)
;; or even
(setq ess-nuke-trailing-whitespace-p t)
;;; Perl
(add-hook 'perl-mode-hook
(lambda () (setq perl-indent-level 4)))
(ess-toggle-underscore nil)
(custom-set-faces
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(default ((t (:inherit nil :stipple nil :background "white" :foreground "black" :inverse-video nil :box nil :strike-through nil :overline nil :underline nil :slant normal :weight normal :height 87 :width normal :foundry "unknown" :family "DejaVu Sans Mono")))))
(show-paren-mode t)
@@ -0,0 +1,14 @@
[user]
email = xie@yihui.name
name = Yihui Xie
[alias]
co = checkout
br = branch
cp = cherry-pick
[gui]
fontui = -family Cantarell -size 10 -weight normal -slant roman -underline 0 -overstrike 0
fontdiff = -family \"Courier 10 Pitch\" -size 9 -weight normal -slant roman -underline 0 -overstrike 0
[branch "master"]
rebase = true
[branch]
autosetuprebase = always
@@ -0,0 +1,8 @@
dist/
/host
*.o
*.so
*.swp
*.po~
/docs
modules/luci-base/src/po2lmo
3 .netrc
@@ -0,0 +1,3 @@
machine win-builder.r-project.org
login anonymous
password foo@bar.com
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