Redo revdep check.

.Rbuildignore

@@ -14,4 +14,3 @@
 ^paper$
 ^CONDUCT\.md$
 ^junk$
-^README\.md$

revdep/README.md

@@ -10,7 +10,7 @@
 |collate  |en_GB.UTF-8                  |
 |ctype    |en_GB.UTF-8                  |
 |tz       |Europe/London                |
-|date     |2019-06-23                   |
+|date     |2019-06-26                   |
 
 # Dependencies
 
@@ -20,12 +20,3 @@
 
 # Revdeps
 
-## New problems (4)
-
-|package                                      |version |error  |warning |note |
-|:--------------------------------------------|:-------|:------|:-------|:----|
-|[autothresholdr](problems.md#autothresholdr) |1.3.3   |__+2__ |        |     |
-|[detrendr](problems.md#detrendr)             |0.6.2   |__+1__ |        |1    |
-|[ijtiff](problems.md#ijtiff)                 |2.0.0   |__+2__ |        |     |
-|[nandb](problems.md#nandb)                   |2.0.2   |__+2__ |        |1    |
-

revdep/checks.noindex/autothresholdr/new/autothresholdr.Rcheck/00check.log

@@ -48,48 +48,15 @@
 * checking compiled code ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... ERROR
-Running examples in ‘autothresholdr-Ex.R’ failed
-The error most likely occurred in:
-
-> ### Name: auto_thresh
-> ### Title: Automatically threshold an array of non-negative integers.
-> ### Aliases: auto_thresh auto_thresh_mask auto_thresh_apply_mask mask
-> ###   apply_mask
-> 
-> ### ** Examples
-> 
-> img_location <- system.file("extdata", "eg.tif", package = "autothresholdr")
-> img <- ijtiff::read_tif(img_location)
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  namespace ‘strex’ 1.1.0 is being loaded, but >= 1.1.1 is required
-Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
-Execution halted
+* checking examples ... OK
 * checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ... ERROR
+* checking tests ... OK
   Running ‘spelling.R’
   Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
   Running ‘testthat.R’
-Running the tests in ‘tests/testthat.R’ failed.
-Last 13 lines of output:
-  11: asNamespace(ns)
-  12: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
-  13: stop(gettextf("namespace %s %s is being loaded, but %s %s is required", sQuote(package), version, 
-         zop, zversion), domain = NA)
-
-  ══ testthat results  ════════════════════════════════════════════════════════════════════════════
-  OK: 0 SKIPPED: 0 WARNINGS: 0 FAILED: 5
-  1. Error: (unknown) (@test_auto_thresh_methods.R#3) 
-  2. Error: mean_stack_thresh works (@test_stack_thresh.R#3) 
-  3. Error: auto_thresh works (@test_thresh.R#4) 
-  4. Error: auto_thresh works with matrices (@test_thresh.R#73) 
-  5. Error: translate_fail works (@test_utils.R#4) 
-
-  Error: testthat unit tests failed
-  Execution halted
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
 * checking running R code from vignettes ... NONE
 * checking re-building of vignette outputs ... SKIPPED
 * DONE
-Status: 2 ERRORs
+Status: OK

revdep/checks.noindex/autothresholdr/new/autothresholdr.Rcheck/00install.out

@@ -4,16 +4,16 @@
 ** libs
 clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/library.noindex/autothresholdr/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c AutoThreshold.cpp -o AutoThreshold.o
 clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/library.noindex/autothresholdr/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
-RcppExports.cpp:201:1: warning: unused variable 'nprot' [-Wunused-variable]
+RcppExports.cpp:201:1: warning: unused variable 'stop_sym' [-Wunused-variable]
 BEGIN_RCPP
 ^
-/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/library.noindex/autothresholdr/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
-    int nprot = 0;                                                                               \
-        ^
-RcppExports.cpp:201:1: warning: unused variable 'stop_sym' [-Wunused-variable]
 /Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/library.noindex/autothresholdr/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
+RcppExports.cpp:201:1: warning: unused variable 'nprot' [-Wunused-variable]
+/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/library.noindex/autothresholdr/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
+    int nprot = 0;                                                                               \
+        ^
 RcppExports.cpp:235:1: warning: unused variable 'nprot' [-Wunused-variable]
 BEGIN_RCPP
 ^

revdep/checks.noindex/autothresholdr/new/autothresholdr.Rcheck/autothresholdr-Ex.Rout

@@ -39,7 +39,133 @@ Type 'q()' to quit R.
 > 
 > img_location <- system.file("extdata", "eg.tif", package = "autothresholdr")
 > img <- ijtiff::read_tif(img_location)
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  namespace ‘strex’ 1.1.0 is being loaded, but >= 1.1.1 is required
-Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
-Execution halted
+Reading eg.tif: an 8-bit, 100x100 pixel image of unsigned
+integer type. Reading 1 channel and 1 frame . . .
+ Done.
+> auto_thresh(img, "huang")
+[1] 5
+attr(,"ignore_black")
+[1] FALSE
+attr(,"ignore_white")
+[1] FALSE
+attr(,"ignore_na")
+[1] FALSE
+attr(,"autothresh_method")
+[1] "Huang"
+attr(,"class")
+[1] "th"      "integer"
+> auto_thresh(img, "tri")
+[1] 3
+attr(,"ignore_black")
+[1] FALSE
+attr(,"ignore_white")
+[1] FALSE
+attr(,"ignore_na")
+[1] FALSE
+attr(,"autothresh_method")
+[1] "Triangle"
+attr(,"class")
+[1] "th"      "integer"
+> auto_thresh(img, "Otsu")
+[1] 13
+attr(,"ignore_black")
+[1] FALSE
+attr(,"ignore_white")
+[1] FALSE
+attr(,"ignore_na")
+[1] FALSE
+attr(,"autothresh_method")
+[1] "Otsu"
+attr(,"class")
+[1] "th"      "integer"
+> auto_thresh(img, 9)
+[1] 9
+attr(,"ignore_black")
+[1] NA
+attr(,"ignore_white")
+[1] NA
+attr(,"ignore_na")
+[1] NA
+attr(,"autothresh_method")
+[1] NA
+attr(,"class")
+[1] "th"      "numeric"
+> mask <- auto_thresh_mask(img, "huang")
+> ijtiff::display(mask[, , 1, 1])
+> masked <- auto_thresh_apply_mask(img, "huang")
+> ijtiff::display(masked[, , 1, 1])
+> masked <- auto_thresh_apply_mask(img, 25)
+> ijtiff::display(masked[, , 1, 1])
+> 
+> 
+> 
+> cleanEx()
+> nameEx("mean_stack_thresh")
+> ### * mean_stack_thresh
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: mean_stack_thresh
+> ### Title: Threshold every image frame in an image stack based on their
+> ###   mean.
+> ### Aliases: mean_stack_thresh
+> 
+> ### ** Examples
+> 
+> img <- ijtiff::read_tif(system.file("extdata", "50.tif",
++   package = "autothresholdr"
++ ))
+Reading 50.tif: an 8-bit, 100x100 pixel image of unsigned
+integer type. Reading 1 channel and 50 frames . . .
+ Done.
+> ijtiff::display(img[, , 1, 1])
+> img_thresh_mask <- mean_stack_thresh(img, "Otsu")
+> ijtiff::display(img_thresh_mask[, , 1, 1])
+> ijtiff::display(img[, , 1, 1])
+> img_thresh_mask <- mean_stack_thresh(img, "Huang")
+> ijtiff::display(img_thresh_mask[, , 1, 1])
+> 
+> 
+> 
+> cleanEx()
+> nameEx("med_stack_thresh")
+> ### * med_stack_thresh
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: med_stack_thresh
+> ### Title: Threshold every image frame in a stack based on their median.
+> ### Aliases: med_stack_thresh
+> 
+> ### ** Examples
+> 
+> img <- ijtiff::read_tif(system.file("extdata", "50.tif",
++   package = "autothresholdr"
++ ))
+Reading 50.tif: an 8-bit, 100x100 pixel image of unsigned
+integer type. Reading 1 channel and 50 frames . . .
+ Done.
+> ijtiff::display(img[, , 1, 1])
+> img_thresh_mask <- med_stack_thresh(img, "Otsu")
+> ijtiff::display(img_thresh_mask[, , 1, 1])
+> ijtiff::display(img[, , 1, 1])
+> img_thresh_mask <- med_stack_thresh(img, "Triangle")
+> ijtiff::display(img_thresh_mask[, , 1, 1])
+> 
+> 
+> 
+> ### * <FOOTER>
+> ###
+> cleanEx()
+> options(digits = 7L)
+> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed:  3.303 0.269 4.218 0 0 
+> grDevices::dev.off()
+null device 
+          1 
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')

revdep/checks.noindex/autothresholdr/new/autothresholdr.Rcheck/tests/spelling.Rout

@@ -25,4 +25,4 @@ All Done!
 > 
 > proc.time()
    user  system elapsed 
-  1.008   0.271   1.358 
+  1.153   0.325   1.737 

revdep/checks.noindex/autothresholdr/new/autothresholdr.Rcheck/tests/testthat.Rout

@@ -0,0 +1,27 @@
+
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin15.6.0 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(testthat)
+> library(autothresholdr)
+> 
+> test_check("autothresholdr")
+══ testthat results  ════════════════════════════════════════════════════════════════════════════
+OK: 69 SKIPPED: 0 WARNINGS: 0 FAILED: 0
+> 
+> proc.time()
+   user  system elapsed 
+  4.180   0.278   5.418