Merge branch 'hotfix/fix-0.8.0-cran-issues'

Fix spelling in DESCRIPTION
Use knitr correctly for vignettes (tar ball includes build folder)

.gitignore

@@ -6,3 +6,7 @@
 *.tar.gz
 *.Rcheck
 revdep
+/inst/doc/introduction.R
+/inst/doc/introduction.html
+/inst/doc/smd.R
+/inst/doc/smd.html

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: tableone
 Type: Package
-Title: Create "Table 1" to Describe Baseline Characteristics
+Title: Create 'Table 1' to Describe Baseline Characteristics
 Version: 0.8.1
 Date: 2017-06-16
 Author: Kazuki Yoshida, Justin Bohn.
 Maintainer: Kazuki Yoshida <[email protected]>
-Description: Creates "Table 1", i.e., description of baseline patient
+Description: Creates 'Table 1', i.e., description of baseline patient
     characteristics, which is essential in every medical research.
     Supports both continuous and categorical variables, as well as
     p-values and standardized mean differences. Weighted data are
-    supported via the survey package. See github for a screencast.
-    tableone was inspired by descriptive statistics functions in
-    Deducer , a Java-based GUI package by Ian Fellows. This package
+    supported via the 'survey' package. See 'github' for a screen cast.
+    'tableone' was inspired by descriptive statistics functions in
+    'Deducer' , a Java-based GUI package by Ian Fellows. This package
     does not require GUI or Java, and intended for command-line users.
 License: GPL-2
 Imports:
@@ -29,9 +29,9 @@ Suggests:
     Matching,
     reshape2,
     ggplot2,
-    rmarkdown,
+    knitr,
     geepack,
     lme4
 URL: https://github.com/kaz-yos/tableone
-VignetteBuilder: rmarkdown
+VignetteBuilder: knitr
 RoxygenNote: 6.0.1

Makefile

@@ -23,7 +23,7 @@ PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(V
 
 ## .PHONY to allow non-file targets (file targets should not be here)
 ## https://www.gnu.org/software/make/manual/html_node/Phony-Targets.html
-.PHONY: test build_win build check revdep install clean
+.PHONY: test winbuild vignettes build check check_devtools revdep install clean
 
 
 ### Define targets
@@ -32,20 +32,23 @@ PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(V
 test: NAMESPACE
 	Rscript -e "options(width = 120); devtools::test()" | tee test-all.txt
 
-## build_win always build regardless of file update status
+## winbuild always build regardless of file update status
 ## Links to results e-mailed (no useful output locally)
-build_win:
+winbuild:
 	Rscript -e "devtools::build_win(version = 'R-devel')"
 	Rscript -e "devtools::build_win(version = 'R-release')"
 
+## Build vignettes in inst/doc
+vignettes:
+	Rscript -e "devtools::build_vignettes()"
+
 ## build depends on the *.tar.gz file, i.e., its own product.
 ## *.tar.gz file is defined seprately to prevent build execution on every invocation.
 build: $(PKG_NAME)_$(PKG_VERSION).tar.gz
 
 ## (file target) The *.tar.gz file depends on package files including NAMESPACE,
 ## and build *.tar.gz file from these.
 $(PKG_NAME)_$(PKG_VERSION).tar.gz: $(PKG_FILES)
-	cp -a ${VIG_FILES} inst/doc/
 	Rscript -e "devtools::build(pkg = '.', path = '.', manual = TRUE)"
 
 ## (file target) NAMESPACE depends on *.R files, and excecute roxygen2 on these.
@@ -55,6 +58,9 @@ NAMESPACE: $(R_FILES)
 
 ## check requires the *.tar.gz file, and execute strict tests on it.
 check: $(PKG_NAME)_$(PKG_VERSION).tar.gz
+	R CMD check --as-cran ./$(PKG_NAME)_$(PKG_VERSION).tar.gz | tee cran-check.txt
+
+check_devtools: $(PKG_NAME)_$(PKG_VERSION).tar.gz
 	Rscript -e "options(width = 120); devtools::check(pkg = '.', check_dir = '.', manual = TRUE)" | tee cran-check.txt
 
 ## revdep requires the *.tar.gz file, and execute strict tests on it.

NEWS

@@ -1,11 +1,15 @@
-tableone 0.8.1 (2017-06-16)
+tableone 0.8.1 (2017-06-17)
 ----------------------------------------------------------------
 
-BUG FIX
+BUG FIXES
 
 * Fix alignment issue with the Missing column. Note currently the
   percentage is shown with 1 decimal and this is hard-coded.
 
+* Change vignetteBuilder to knitr to form the index correctly.
+
+* Single-quote package names in DESCRIPTION.
+
 
 tableone 0.8.0 (2017-06-15)
 ----------------------------------------------------------------

cran-check.txt

@@ -1,9 +1,3 @@
-* checking for file ‘/Users/kazuki/Documents/programming/r/tableone/DESCRIPTION’ ... OK
-* preparing ‘tableone’:
-* checking DESCRIPTION meta-information ... OK
-* checking for LF line-endings in source and make files
-* checking for empty or unneeded directories
-* building ‘tableone_0.8.1.tar.gz’
 * using log directory ‘/Users/kazuki/Documents/programming/r/tableone/tableone.Rcheck’
 * using R version 3.4.0 (2017-04-21)
 * using platform: x86_64-apple-darwin15.6.0 (64-bit)
@@ -12,6 +6,8 @@
 * checking for file ‘tableone/DESCRIPTION’ ... OK
 * checking extension type ... Package
 * this is package ‘tableone’ version ‘0.8.1’
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+Maintainer: ‘Kazuki Yoshida <[email protected]>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -23,6 +19,7 @@
 * checking whether package ‘tableone’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
+* checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -35,6 +32,7 @@
 * checking whether the package can be unloaded cleanly ... OK
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
+* checking use of S3 registration ... OK
 * checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
@@ -55,7 +53,9 @@
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ...
  OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * DONE
 Status: OK
-

cran-comment.md

@@ -1,22 +1,27 @@
 ## What's new
 The following changes are included.
 
-tableone 0.8.1 (2017-06-16)
+tableone 0.8.1 (2017-06-17)
 ----------------------------------------------------------------
 BUG FIX
 * Fix alignment issue with the Missing column. Note currently the
   percentage is shown with 1 decimal and this is hard-coded.
+* Change vignetteBuilder to knitr to form the index correctly.
+* Single-quote package names in DESCRIPTION.
+
 
 ## Test environments
 * Local OS X 10.12.5, R 3.4.0
 * Ubuntu Linux on Travis-CI (oldrel, release, and devel)
 * win-builder (release and devel)
 
+
 ## R CMD check results
 * ERRORs: None
 * WARNINGs: None
-* NOTEs:
- - Author e-mail check
+* NOTEs: None
+
 
 ## Downstream dependencies
-RcmdrPlugin.EZR GUI frontend: No change was made to APIs.
+Checked RcmdrPlugin.EZR: 0 errors | 0 warnings | 0 notes
+Checked rpsftm         : 0 errors | 0 warnings | 0 notes

inst/doc/introduction.Rmd

@@ -162,5 +162,5 @@ print(tab3$ContTable, nonnormal = biomarkers)
 
 --------------------
 - Authored by Kazuki Yoshida
-- CRAN page: http://cran.r-project.org/package=tableone
+- CRAN page: https://cran.r-project.org/package=tableone
 - github page: https://github.com/kaz-yos/tableone

inst/doc/smd.Rmd

@@ -152,7 +152,7 @@ addmargins(table(ExtractSmd(tabMatched) > 0.1))
 
 ## Propensity score matching weight
 
-The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). An earlier version of the paper is available free (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.359.4724&rep=rep1&type=pdf ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full .
+The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full .
 
 ```{r}
 
@@ -254,5 +254,5 @@ print(resTogether, quote = FALSE)
 
 --------------------
 - Authored by Kazuki Yoshida
-- CRAN page: http://cran.r-project.org/package=tableone
+- CRAN page: https://cran.r-project.org/package=tableone
 - github page: https://github.com/kaz-yos/tableone

tableone.Rcheck/tableone-Ex.Rout

@@ -3316,7 +3316,7 @@ detaching ‘package:survey’, ‘package:survival’, ‘package:Matrix’,
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  7.4 0.285 8.882 0.005 0.005 
+Time elapsed:  9.407 0.276 9.755 0.006 0.005 
 > grDevices::dev.off()
 null device 
           1 

vignettes/introduction.Rmd

@@ -162,5 +162,5 @@ print(tab3$ContTable, nonnormal = biomarkers)
 
 --------------------
 - Authored by Kazuki Yoshida
-- CRAN page: http://cran.r-project.org/package=tableone
+- CRAN page: https://cran.r-project.org/package=tableone
 - github page: https://github.com/kaz-yos/tableone

vignettes/smd.Rmd

@@ -152,7 +152,7 @@ addmargins(table(ExtractSmd(tabMatched) > 0.1))
 
 ## Propensity score matching weight
 
-The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). An earlier version of the paper is available free (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.359.4724&rep=rep1&type=pdf ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full .
+The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full .
 
 ```{r}
 
@@ -254,5 +254,5 @@ print(resTogether, quote = FALSE)
 
 --------------------
 - Authored by Kazuki Yoshida
-- CRAN page: http://cran.r-project.org/package=tableone
+- CRAN page: https://cran.r-project.org/package=tableone
 - github page: https://github.com/kaz-yos/tableone