Making amenable to R CMD check

.Rbuildignore

@@ -1 +1,8 @@
+^\.Rhistory$
+^misc$
+^README\.Rmd$
+^appveyor\.yml$
+^\.travis\.yml$
+^RBioFormats\.Rproj$
+^\.Rproj\.user$
 ^man-roxygen$

.gitignore

@@ -0,0 +1,3 @@
+inst/java/bioformats_package.jar
+.Rhistory
+.Rproj.user

.travis.yml

@@ -0,0 +1,55 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: false
+cache: packages
+warnings_are_errors: true
+use_bioc: true
+bioc_required: true
+cran: http://cran.rstudio.com
+
+addons:
+  apt:
+    packages:
+    - libfftw3-dev
+    - libgsl0-dev
+    - libgsl0ldbl
+
+os:
+  - linux
+  - osx
+osx_image: xcode9 
+
+
+env:
+  global: 
+    - RGL_USE_NULL=TRUE
+    - DISPLAY=:99.0
+r_check_args: --as-cran --install-args=--build
+
+before_install:
+  - export PROJ_DIR=`basename $PWD`    
+  - fname=travis_helpers.sh
+  - wget -O ${fname} http://bit.ly/travis_helpers
+  - cat ${fname}; source ${fname}; rm ${fname}  
+  - cat DESCRIPTION
+  - start_xvfb ;
+  - export rver=`r_version`; echo $rver ;
+  - if [ "$TRAVIS_OS_NAME" = "osx" ];
+    then
+      no_open_mp ; 
+    fi
+  - jags_install  
+  - export PACKAGE_NAME=`package_name`
+  - echo "Package Name is $PACKAGE_NAME"
+  - fftw_install ;
+  - R CMD javareconf ;
+
+after_success:
+  - cat ${PACKAGE_NAME}.Rcheck/00install.out
+  - cat ${PACKAGE_NAME}.Rcheck/00check.log
+
+after_failure:
+  - cat ${PACKAGE_NAME}.Rcheck/00install.out
+  - cat ${PACKAGE_NAME}.Rcheck/00check.log
+

DESCRIPTION

@@ -2,7 +2,8 @@ Package: RBioFormats
 Version: 0.0.53
 BioFormats: 5.9.2
 Title: R interface to Bio-Formats
-Description: An R package which interfaces the OME Bio-Formats Java library to
+Description: An R package which interfaces the OME Bio-Formats 
+    <https://www.openmicroscopy.org/bio-formats/> Java library to
     allow reading of proprietary image data and metadata.
 Encoding: UTF-8
 Author: Andrzej Oleś
@@ -34,4 +35,7 @@ Collate:
     'utils.R'
     'write.image.R'
     'zzz.R'
-RoxygenNote: 6.0.1
+biocViews:
+RoxygenNote: 6.1.0
+BugReports: https://github.com/aoles/RBioFormats/issues
+URL: https://github.com/aoles/RBioFormats

R/zzz.R

@@ -1,51 +1,56 @@
+.onAttach <- function(lib, pkg) {
+
+
+  msg <- sprintf("BioFormats library version %s", BioFormats.version())
+  packageStartupMessage(msg)
+
+}
+
 .onLoad <- function(lib, pkg) {
+
   ## check whether called on a source package directory which has a different
   ## path to .jar files compared to the installed package (this workaround is
   ## needed, e.g., to run devtools::test)
   pkg_dir <- file.path(lib, pkg)
   installed <- getwd() != pkg_dir
-  
+
   jar_dir <-
     if (installed)
       file.path(pkg_dir, "java")
-    else
-      jar_dir = file.path(pkg_dir, "inst", "java")
-  
+  else
+    jar_dir = file.path(pkg_dir, "inst", "java")
+
   tryCatch(download_bioformats(pkg_dir, jar_dir),
-           error = function(e) 
+           error = function(e)
              stop("failed to download Bio-Formats Java library.\n  Check your internet connection and try again.", call.=FALSE)
-           )
-  
+  )
+
   jars =
     if (installed)
-      "" 
-    else
-      list.files(jar_dir, pattern = ".*\\.jar", full.names = TRUE)
-  
+      ""
+  else
+    list.files(jar_dir, pattern = ".*\\.jar", full.names = TRUE)
+
   .jpackage(pkg, lib.loc = lib, morePaths = jars)
-
-  msg <- sprintf("BioFormats library version %s", BioFormats.version())
-  packageStartupMessage(msg)
-
   FormatTools <<- J("loci.formats.FormatTools")
 }
 
 download_bioformats <- function (pkg_dir, jar_dir) {
-  ver <- read.dcf(file.path(pkg_dir, "DESCRIPTION"), "BioFormats")
+  ver <- read.dcf(file.path(pkg_dir, "DESCRIPTION"), fields = "BioFormats")
   jar <- "bioformats_package.jar"
   url_template <- "https://downloads.openmicroscopy.org/bio-formats/%s/artifacts/%s"
   jar_url <- sprintf(url_template, ver, jar)
   jar_dst <- file.path(jar_dir, jar)
-  
+
   if ( file.exists(jar_dst) ) {
     md5_local <- tools::md5sum(jar_dst)
     md5_file <- readLines(paste(jar_url, "md5", sep="."))
-    md5_remote <- sub("([0-9a-z]+).*", "\\1", md5_file)    
+    md5_remote <- sub("([0-9a-z]+).*", "\\1", md5_file)
     if ( md5_local == md5_remote )
       return(FALSE)
   }
-  
+
   utils::download.file(jar_url, jar_dst, quiet=FALSE)
-  
+
   return(TRUE)
 }

RBioFormats.Rproj

@@ -0,0 +1,22 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,collate,namespace

README.Rmd

@@ -0,0 +1,99 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+```{r, include=FALSE}
+if (requireNamespace("git2r")) {
+  repo = git2r::repository(".")
+  url = git2r::remote_url(repo, remote = "origin") 
+  gh_user = basename(dirname(url))
+  gh_package = basename(url)
+} else {
+  gh_user = "aoles"
+  gh_package = "RBioFormats"
+}
+```
+
+[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/`r gh_user`/`r gh_package`.svg?branch=master&svg=true)](https://ci.appveyor.com/project/`r gh_user`/`r gh_package`)
+[![Travis build status](https://travis-ci.com/`r gh_user`/`r gh_package`.svg?branch=master)](https://travis-ci.com/`r gh_user`/`r gh_package`)  
+
+## Installation
+
+First, make sure you have [JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.7 or higher installed.
+To install *RBioFormats* use the `biocLite` installation script in order to resolve the dependency on the Bioconductor package *[EBImage](http://biocondcutor.org/packages/EBImage)*.
+
+```r
+source("https://bioconductor.org/biocLite.R")
+biocLite("aoles/RBioFormats") # You might need to first run `install.packages("devtools")`
+```
+
+### Mac OS X
+
+Mac OS comes with a legacy Apple Java 6. In order to use *RBioFormats*, you will need to update your Java installation to a newer version provided by Oracle.
+
+1. Install [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html).
+
+2. Update R Java configuration by executing from the command line (you might have to run it as a super user by prepending `sudo` depending on your installation).
+```
+R CMD javareconf
+```
+
+3. Re-install *rJava* from sources in order to properly link to the non-system
+Java installation.
+```r
+install.packages("rJava", type="source")
+```
+
+You can verify your configuration by running the following commands. This should return the Java version string corresponding to the one downloaded and installed in step 1.
+
+```r
+library(rJava)
+.jinit()
+.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
+## [1] "1.8.0_112-b16" 
+```
+
+## Documentation
+
+For example use, see the [package vignette](https://rawgit.com/aoles/RBioFormats/master/vignettes/RBioFormats.html).
+
+## FAQ
+
+See my [answers on Stack Overflow](http://stackoverflow.com/search?q=user:A2792099+rbioformats).
+
+## Caveats
+
+### The `java.lang.OutOfMemoryError` error
+
+If you get the `java.lang.OutOfMemoryError: Java heap space` error, try increasing the maximum heap size by supplying the -Xmx parameter before the Java Virtual Machine is initialized. For example, use
+
+```r
+options( java.parameters = "-Xmx4g" )
+library( "RBioFormats" )
+```
+
+to override the default setting and assign 4 gigabytes of heap space to the Java environment.
+
+Information about the current Java heap space limit can be retrieved by `checkJavaMemory()`.
+
+### Use with BiocParallel
+
+Each R process needs a separate JVM instance. For this, load the package in the parallelized function, e.g.,
+
+```r
+bplapply (files, function(f) {
+  library(RBioFormats)
+  ...
+})
+```