Ready for CRAN v3.2.0.

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: filesstrings
 Title: Handy File and String Manipulation
-Version: 3.1.7
+Version: 3.2.0
 Authors@R: 
     c(person(given = "Rory",
              family = "Nolan",
@@ -33,7 +33,7 @@ Imports:
     magrittr (>= 1.5),
     purrr (>= 0.3.0),
     rlang (>= 0.3.3),
-    strex (>= 1.3.1),
+    strex (>= 1.4),
     stringi (>= 1.5),
     withr (>= 2.1.0)
 Suggests: 

NEWS.md

@@ -1,3 +1,9 @@
+# `filesstrings` 3.2.0
+
+## BUG FIXES
+* Insist on `strex` >= 1.4 which has improved argument matching.
+
+
 # `filesstrings` 3.1.7
 
 ## BUG FIXES

codemeta.json

@@ -10,7 +10,7 @@
   "codeRepository": "https://github.com/rorynolan/filesstrings",
   "issueTracker": "https://github.com/rorynolan/filesstrings/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "3.1.7",
+  "version": "3.2.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -211,7 +211,7 @@
       "@type": "SoftwareApplication",
       "identifier": "strex",
       "name": "strex",
-      "version": ">= 1.3.1",
+      "version": ">= 1.4",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -284,6 +284,6 @@
     }
   ],
   "relatedLink": "https://CRAN.R-project.org/package=filesstrings",
-  "fileSize": "52440.958KB",
+  "fileSize": "51931.148KB",
   "readme": "https://github.com/rorynolan/filesstrings/blob/master/README.md"
 }

revdep/README.md

@@ -10,14 +10,16 @@
 |collate  |en_GB.UTF-8                  |
 |ctype    |en_GB.UTF-8                  |
 |tz       |Europe/London                |
-|date     |2020-09-21                   |
+|date     |2020-10-10                   |
 
 # Dependencies
 
-|package      |old   |new        |Δ  |
-|:------------|:-----|:----------|:--|
-|filesstrings |3.1.6 |3.1.7      |*  |
-|crayon       |NA    |1.3.4.9000 |*  |
+|package      |old   |new   |Δ  |
+|:------------|:-----|:-----|:--|
+|filesstrings |3.1.7 |3.1.7 |   |
+|rlang        |NA    |0.4.8 |*  |
+|strex        |1.4.0 |1.4.0 |   |
+|withr        |NA    |2.3.0 |*  |
 
 # Revdeps
 

revdep/checks.noindex/ijtiff/new/ijtiff.Rcheck/00check.log → revdep/checks.noindex/SSHAARP/new/SSHAARP.Rcheck/00check.log

@@ -1,11 +1,10 @@
-* using log directory ‘/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/checks.noindex/ijtiff/new/ijtiff.Rcheck’
+* using log directory ‘/Users/rnolan/Dropbox/DPhil/Misc/RStuff/filesstrings/revdep/checks.noindex/SSHAARP/new/SSHAARP.Rcheck’
 * using R version 4.0.2 (2020-06-22)
 * using platform: x86_64-apple-darwin17.0 (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-manual --no-build-vignettes’
-* checking for file ‘ijtiff/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘ijtiff’ version ‘2.2.0’
+* checking for file ‘SSHAARP/DESCRIPTION’ ... OK
+* this is package ‘SSHAARP’ version ‘1.0.1’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -15,7 +14,7 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking whether package ‘ijtiff’ can be installed ... OK
+* checking whether package ‘SSHAARP’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking ‘build’ directory ... OK
@@ -31,7 +30,10 @@
 * 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 dependencies in R code ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... NOTE
+Namespace in Imports field not imported from: ‘sessioninfo’
+  All declared Imports should be used.
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
@@ -44,28 +46,16 @@
 * checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
-* checking line endings in shell scripts ... OK
-* checking line endings in C/C++/Fortran sources/headers ... OK
-* checking line endings in Makefiles ... OK
-* checking compilation flags in Makevars ... OK
-* checking for GNU extensions in Makefiles ... OK
-* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
-* checking use of PKG_*FLAGS in Makefiles ... OK
-* checking compiled code ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
 * checking examples ... OK
-* checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ... OK
-  Running ‘spelling.R’
-  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
-  Running ‘testthat.R’
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
 * checking running R code from vignettes ... NONE
-  ‘reading-and-writing-images.Rmd’ using ‘UTF-8’... OK
-  ‘text-images.Rmd’ using ‘UTF-8’... OK
-  ‘the-imagej-problem.Rmd’ using ‘UTF-8’... OK
+  ‘vignette.Rmd’ using ‘UTF-8’... OK
 * checking re-building of vignette outputs ... SKIPPED
 * DONE
-Status: OK
+Status: 1 NOTE

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

@@ -0,0 +1,16 @@
+* installing *source* package ‘SSHAARP’ ...
+** package ‘SSHAARP’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** inst
+** byte-compile and prepare package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** installing vignettes
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (SSHAARP)

revdep/checks.noindex/SSHAARP/new/SSHAARP.Rcheck/SSHAARP-Ex.R

@@ -0,0 +1,100 @@
+pkgname <- "SSHAARP"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+library('SSHAARP')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("BLAASD")
+### * BLAASD
+
+flush(stderr()); flush(stdout())
+
+### Name: BLAASD
+### Title: BLAASD - Build Loci Amino Acid Specific Dataframe
+### Aliases: BLAASD
+
+### ** Examples
+
+#BLAASD with one locus as input
+
+#BLAASD with multiple loci as input
+
+
+
+cleanEx()
+nameEx("PALM")
+### * PALM
+
+flush(stderr()); flush(stdout())
+
+### Name: PALM
+### Title: Population Allele Locating Mapmaker
+### Aliases: PALM
+
+### ** Examples
+
+#example to produce a color frequency heat map where migrant populations are filtered out
+PALM("DRB1*26F~28E~30Y",filename = solberg_dataset[85:100,], filterMigrant=TRUE)
+#example to produce a greyscale heat map where migrant populations are not filtered out
+PALM("DRB1*26F~28E~30Y", filename = solberg_dataset[85:100,], color=FALSE, filterMigrant=FALSE)
+
+
+
+
+cleanEx()
+nameEx("checkMotif")
+### * checkMotif
+
+flush(stderr()); flush(stdout())
+
+### Name: checkMotif
+### Title: Syntactic and semantic validation of HLA amino acid motifs
+### Aliases: checkMotif
+
+### ** Examples
+
+#Example where a motif is formatted correctly
+
+#Example where format is incorrect
+
+#Example where an amino acid position does not exist
+
+
+
+cleanEx()
+nameEx("findMotif")
+### * findMotif
+
+flush(stderr()); flush(stdout())
+
+### Name: findMotif
+### Title: Returns an alignment data frame of alleles that share a specific
+###   amino acid motif
+### Aliases: findMotif
+
+### ** Examples
+
+
+#example with actual motif
+
+#example with non-existent motif
+
+#extracting names of alleles with user-defined motif
+findMotif("DRB1*26F~28E~30Y")[,4]
+
+
+
+### * <FOOTER>
+###
+cleanEx()
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')