make vol2birdR suggested (#565)

* Change rsl to NEXRAD in message

* Updated message untill vol2bird r is released

* Update hooks.R

Installation instructions are now with `check_installed`

* refer to vol2birdR install instructions website

* Update system requirements message

* don't warn about system dependencies on intel macs, which have pre-compiled binary available

* shorten dependency warning

---------

Co-authored-by: Adriaan Dokter

DESCRIPTION

@@ -46,15 +46,14 @@ Imports:
     utils,
     viridisLite,
     viridis,
-    vol2birdR
+    rlang
 Remotes:
-    adokter/vol2birdR,
     bioc::rhdf5
 Suggests:
+    vol2birdR,
     aws.s3,
     ggmap (>= 3.0.0),
     knitr,
-    rlang,
     tidyselect,
     rmarkdown,
     testthat,

R/apply_mistnet.R

@@ -132,7 +132,7 @@ apply_mistnet_body <- function(file, pvolfile_out, verbose = FALSE,
                           local_install, local_mistnet) {
 
   assert_that(file.exists(file))
-
+  rlang::check_installed('vol2birdR',format_reason_vol2bird("to run `apply_mist`."))
   if (!vol2birdR::mistnet_exists()) {
     stop("MistNet has not been installed, see vol2birdR package documentation for install instructions")
   }

R/bioRad-deprecated.R

@@ -34,6 +34,7 @@ update_docker <- function(...) {
 #' @export
 vol2bird_version <- function(...) {
   .Deprecated("vol2birdR::vol2bird_version")
+  rlang::check_installed('vol2birdR',format_reason_vol2bird("to run `vol2bird_version`."))
   warning("vol2bird_version has been moved to package vol2birdR")
   vol2birdR::vol2bird_version()
 }

R/calculate_vp.R

@@ -204,7 +204,7 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
       vpfile = vpfile, pvolfile_out = pvolfile_out,
       autoconf = autoconf, verbose = verbose, warnings = warnings,
       mount = mount, sd_vvp_threshold = sd_vvp_threshold,
-      rcs = rcs, dual_pol = dual_pol, rho_hv = rho_hv, single_pol=single_pol,
+      rcs = rcs, dual_pol = dual_pol, rho_hv = rho_hv, single_pol = single_pol,
       elev_min = elev_min, elev_max = 90, azim_min = 0, azim_max = 360,
       range_min = range_min, range_max = range_max, n_layer = n_layer,
       h_layer = h_layer, dealias = dealias,
@@ -219,7 +219,7 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
     file.remove(tmp_pvol_file)
     return(res)
   }
-
+  rlang::check_installed("vol2birdR", format_reason_vol2bird("to run `calculate_vp`."))
   # check input arguments
   assert_that(
     is.character(file),
@@ -237,25 +237,24 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
   if (!is.logical(mistnet)) {
     stop("`mistnet` must be a logical value.")
   }
-  if (mistnet){
-    if(missing(local_mistnet)){
+  if (mistnet) {
+    if (missing(local_mistnet)) {
       if (!vol2birdR::mistnet_exists()) {
         stop("MistNet has not been installed, see vol2birdR package documentation for install instructions.")
       }
-    }
-    else{
-      if(!file.exists(local_mistnet)){
-        stop(paste0("'",local_mistnet,"' does not exist, `local_mistnet` should specify the path of MistNet segmentation model"))
+    } else {
+      if (!file.exists(local_mistnet)) {
+        stop(paste0("'", local_mistnet, "' does not exist, `local_mistnet` should specify the path of MistNet segmentation model"))
       }
     }
   }
   if (!is.logical(dealias)) {
     stop("`dealias` must be a logical value.")
   }
-  if(!missing(mount))  {
+  if (!missing(mount)) {
     warning("mount argument is deprecated")
   }
-  if(!missing(local_install)){
+  if (!missing(local_install)) {
     warning("local_install argument is deprecated")
   }
 
@@ -333,7 +332,8 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
   assert_that(is.flag(mistnet))
   assert_that(
     !(mistnet && !vol2birdR::mistnet_exists() && missing(local_mistnet)),
-    msg = "Can't find MistNet installation, see vol2birdR package for install instructions.")
+    msg = "Can't find MistNet installation, see vol2birdR package for install instructions."
+  )
   assert_that(is.flag(dealias))
 
   filedir <- dirname(normalizePath(file[1], winslash = "/"))
@@ -342,7 +342,7 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
   profile.tmp <- tempfile()
 
   config <- vol2birdR::vol2bird_config()
-  if(!autoconf){
+  if (!autoconf) {
     config$birdRadarCrossSection <- rcs
     config$rhohvThresMin <- rho_hv
     config$elevMin <- elev_min
@@ -358,16 +358,16 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
     config$dualPol <- dual_pol
     config$dealiasVrad <- dealias
     if (!missing(sd_vvp_threshold)) config$stdDevMinBird <- sd_vvp_threshold
-  } else{
+  } else {
     # setting stdDevMinBird triggers it to be set according to wavelength (1 m/s for S-band, 2 m/s for C-band)
     config$stdDevMinBird <- -1
   }
   config$mistNetElevs <- mistnet_elevations
   config$useMistNet <- mistnet
-  if(!missing(local_mistnet) & mistnet) config$mistNetPath <- local_mistnet
+  if (!missing(local_mistnet) & mistnet) config$mistNetPath <- local_mistnet
 
   # run vol2bird
-  vol2birdR::vol2bird(file=file, config=config, vpfile=profile.tmp, pvolfile_out=pvolfile_out, verbose = verbose)
+  vol2birdR::vol2bird(file = file, config = config, vpfile = profile.tmp, pvolfile_out = pvolfile_out, verbose = verbose)
 
   # read output into a vp object
   output <- read_vpfiles(profile.tmp)
@@ -380,3 +380,13 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
 
   output
 }
+
+format_reason_vol2bird <- function(x) {
+  on_intel_mac <- Sys.info()[["sysname"]]=="Darwin" & Sys.info()[["machine"]] == "x86_64"
+  if (.Platform$OS.type == "unix" & !on_intel_mac) {
+    return(paste(x, "Installation may require pre-installation of additional system libraries, see https://github.com/adokter/vol2birdR#install for instructions."))
+  } else {
+    # platform is Windows or Intel Mac, pre-compiled binaries are available on CRAN
+    return(x)
+  }
+}

R/hooks.R

@@ -1,9 +1,10 @@
 .onLoad <- function(libname, pkgname) {
   register_all_s3_methods() # dynamically registers non-imported pkgs (tidyverse) # nocov
-  assert_that(is.string(find.package("vol2birdR", verbose=F, quiet=T)),msg="package vol2birdR not found. See https://adokter.github.io/vol2birdR/ for install instructions")
 }
 
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage(paste("Welcome to", pkgname, "version", packageVersion(pkgname)))
-  packageStartupMessage(paste("using vol2birdR version ", packageVersion("vol2birdR"), ifelse(vol2birdR::mistnet_exists(), " (MistNet installed)", " (MistNet not installed)"), sep = ""))
+  if (rlang::is_installed("vol2birdR")) {
+    packageStartupMessage(paste("using vol2birdR version ", packageVersion("vol2birdR"), ifelse(vol2birdR::mistnet_exists(), " (MistNet installed)", " (MistNet not installed)"), sep = ""))
+  }
 }

R/nexrad_odim.R

@@ -37,6 +37,7 @@
 nexrad_to_odim <- function(pvolfile_nexrad, pvolfile_odim, verbose = FALSE) {
   assert_that(dir.exists(dirname(pvolfile_odim)),msg=paste("output directory", dirname(pvolfile_odim), "not found"))
   assert_that(is.writeable(dirname(pvolfile_odim)))
+  rlang::check_installed('vol2birdR',format_reason_vol2bird('to run `nexrad_to_odim`.'))
 
   config <- vol2birdR::vol2bird_config()
   vol2birdR::rsl2odim(file=pvolfile_nexrad, config=config, pvolfile_out=pvolfile_odim, verbose=verbose)

R/read_pvolfile.R

@@ -72,19 +72,20 @@ read_pvolfile <- function(file, param = c(
                           sort = TRUE, lat, lon, height, elev_min = 0,
                           elev_max = 90, verbose = TRUE,
                           mount = dirname(file), local_install) {
-  if(!missing(local_install)) warning("argument 'local_install' has been deprecated")
-  if(!file.exists(file)){
-     stop(paste0("'",file,"' does not exist in current working directory ('",getwd(),"')."))
-  }
-  tryCatch(read_pvolfile_body(
-    file, param, sort, lat, lon,
-    height, elev_min, elev_max,
-    verbose, mount, local_install
-  ),
-  error = function(err) {
-    rhdf5::h5closeAll()
-    stop(err)
+  if (!missing(local_install)) warning("argument 'local_install' has been deprecated")
+  if (!file.exists(file)) {
+    stop(paste0("'", file, "' does not exist in current working directory ('", getwd(), "')."))
   }
+  tryCatch(
+    read_pvolfile_body(
+      file, param, sort, lat, lon,
+      height, elev_min, elev_max,
+      verbose, mount, local_install
+    ),
+    error = function(err) {
+      rhdf5::h5closeAll()
+      stop(err)
+    }
   )
 }
 
@@ -125,9 +126,9 @@ read_pvolfile_body <- function(file, param = c(
     }
   } else {
     pvol_tmp <- tempfile()
-
+    rlang::check_installed("vol2birdR", format_reason_vol2bird("to read `NEXRAD` files."))
     config <- vol2birdR::vol2bird_config()
-    vol2birdR::rsl2odim(file=file, config=config, pvolfile_out=pvol_tmp, verbose=verbose)
+    vol2birdR::rsl2odim(file = file, config = config, pvolfile_out = pvol_tmp, verbose = verbose)
 
     if (!is.pvolfile(pvol_tmp)) {
       file.remove(pvol_tmp)
@@ -168,9 +169,9 @@ read_pvolfile_body <- function(file, param = c(
   }
 
   # construct wavelength attribute from frequency attribute if possible:
-  if(is.null(attribs.how$wavelength) & !is.null(attribs.how$frequency)){
-    speed_of_light = 299792458
-    attribs.how$wavelength = 100*speed_of_light/attribs.how$frequency
+  if (is.null(attribs.how$wavelength) & !is.null(attribs.how$frequency)) {
+    speed_of_light <- 299792458
+    attribs.how$wavelength <- 100 * speed_of_light / attribs.how$frequency
   }
 
   vol.lat <- c(attribs.where$lat) # need the c() to convert single element matrix to single element vector
@@ -218,7 +219,7 @@ read_pvolfile_body <- function(file, param = c(
   datetime <- as.POSIXct(paste(attribs.what$date, attribs.what$time),
     format = "%Y%m%d %H%M%S", tz = "UTC"
   )
-  if(is.null(attribs.what$source)) attribs.what$source=""
+  if (is.null(attribs.what$source)) attribs.what$source <- ""
   sources <- strsplit(attribs.what$source, ",")[[1]]
   radar <- gsub("NOD:", "", sources[which(grepl("NOD:", sources))])
   if (length(radar) == 0) {
@@ -254,8 +255,8 @@ read_pvolfile_body <- function(file, param = c(
   # filter out NULL output from read_pvolfile_scan
   valid_scans <- which(!sapply(data, is.null))
   assert_that(length(valid_scans) > 0, msg = paste("none of the requested scan parameters found in file", file))
-  if(length(valid_scans) < length(scans)){
-    warning(paste("ignoring",length(scans)-length(valid_scans),"scan(s) in file",file,"because requested scan parameter(s) are missing."))
+  if (length(valid_scans) < length(scans)) {
+    warning(paste("ignoring", length(scans) - length(valid_scans), "scan(s) in file", file, "because requested scan parameter(s) are missing."))
   }
   data <- data[valid_scans]
 
@@ -349,7 +350,7 @@ read_pvolfile_scan <- function(file, scan, param, radar, datetime, geo, attribut
   names(quantities) <- quantityNames
 
   # if wavelength is attribute is missing at the scan level, copy it from the pvol level
-  if(is.null(attribs.how$wavelength)) attribs.how$wavelength = attributes$how$wavelength
+  if (is.null(attribs.how$wavelength)) attribs.how$wavelength <- attributes$how$wavelength
 
   output <- list(
     radar = radar, datetime = datetime, params = quantities,
@@ -370,12 +371,14 @@ read_pvolfile_quantity <- function(file, quantity, radar, datetime, geo, dtype)
   data <- replace(data, data == as.numeric(attr$nodata), NA)
   data <- replace(data, data == as.numeric(attr$undetect), NaN)
   data <- as.numeric(attr$offset) + as.numeric(attr$gain) * data
-  if(attr$quantity == "RHOHV"){
+  if (attr$quantity == "RHOHV") {
     data <- replace(data, data > 10, NaN)
   }
-  conversion <- list(gain = as.numeric(attr$gain), offset = as.numeric(attr$offset),
-                     nodata = as.numeric(attr$nodata), undetect = as.numeric(attr$undetect),
-                     dtype = dtype)
+  conversion <- list(
+    gain = as.numeric(attr$gain), offset = as.numeric(attr$offset),
+    nodata = as.numeric(attr$nodata), undetect = as.numeric(attr$undetect),
+    dtype = dtype
+  )
   class(data) <- c("param", class(data))
   attributes(data)$radar <- radar
   attributes(data)$datetime <- datetime

R/zzz.R

@@ -19,9 +19,11 @@ is.nan.data.frame <- function(x) do.call(cbind, lapply(x, is.nan))
 #' Inspired by <https://testthat.r-lib.org/articles/skipping.html#helpers>.
 #'
 #' @keywords internal
-skip_if_no_mistnet <- function() {
-  if (vol2birdR::mistnet_exists()) {
-    return(invisible(TRUE))
+skip_if_no_mistnet <- function(){
+  if(rlang::is_installed('vol2birdR')){
+    if (vol2birdR::mistnet_exists()) {
+      return(invisible(TRUE))
+    }
   }
   testthat::skip("No MistNet")
 }