all read.*() functions now check for empty files

NAMESPACE

@@ -257,6 +257,7 @@ export(abbreviateTimeLabels,
        read.adp,
        read.adp.ad2cp,
        read.adp.rdi,
+       read.adp.nortek,
        read.adp.sontek,
        read.adp.sontek.serial,
        read.adv,

R/adp.nortek.R

@@ -557,6 +557,8 @@ read.adp.ad2cp <- function(file, from=1, to=0, by=1, tz=getOption("oceTz"),
                            monitor=FALSE, despike=FALSE, processingLog,
                            debug=getOption("oceDebug"), ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (!missing(orientation))
         warning("ignoring 'orientation' (see documentation)")
     if (!missing(distance))
@@ -600,8 +602,6 @@ read.adp.ad2cp <- function(file, from=1, to=0, by=1, tz=getOption("oceTz"),
     if (to == 0)
         to <- 1e9                      # this should be enough to read any file
     if (is.character(file)) {
-        if (0 == file.info(file)$size)
-            stop("empty file")
         filename <- fullFilename(file)
         file <- file(file, "rb")
         on.exit(close(file))
@@ -2184,6 +2184,8 @@ read.aquadopp <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                           monitor=FALSE, despike=FALSE, processingLog,
                           debug=getOption("oceDebug"), ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     return(read.adp.nortek(file, from=from, to=to, by=by, tz=tz,
                            longitude=longitude, latitude=latitude,
                            type="aquadopp", orientation=orientation, distance=distance,
@@ -2237,6 +2239,8 @@ read.aquadoppHR <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                             monitor=FALSE, despike=FALSE, processingLog,
                             debug=getOption("oceDebug"), ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     return(read.adp.nortek(file, from=from, to=to, by=by, tz=tz,
                            longitude=longitude, latitude=latitude,
                            type="aquadoppHR",
@@ -2291,6 +2295,8 @@ read.aquadoppProfiler <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                                   monitor=FALSE, despike=FALSE, processingLog,
                                   debug=getOption("oceDebug"), ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     return(read.adp.nortek(file, from=from, to=to, by=by, tz=tz,
                            longitude=longitude, latitude=latitude,
                            type="aquadoppProfiler",
@@ -2338,6 +2344,8 @@ read.adp.nortek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                             debug=getOption("oceDebug"),
                             ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ##degToRad <- atan2(1, 1) / 45
     profileStart <- NULL # prevents scope warning in rstudio; defined later anyway
     bisectAdpNortek <- function(buf, t.find, add=0, debug=0) {

R/adp.sontek.R

@@ -25,6 +25,8 @@ read.adp.sontek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                             debug=getOption("oceDebug"),
                             ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     missing.to <- missing(to)
     ## In this function, comments in [] refer to logical page number of ADPManual_v710.pd; add 14 for file page number
     profileStart <- NULL # prevent scope warning from rstudio; defined later anyway
@@ -439,6 +441,8 @@ read.adp.sontek.serial <- function(file, from=1, to, by=1, tz=getOption("oceTz")
                                    monitor=FALSE, processingLog,
                                    debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ## Data format is described in
     ##   SonTek/YSI
     ##   ADPManual_v710.pdf

R/adv.R

@@ -351,6 +351,8 @@ read.adv <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                      start=NULL, deltat=NA,
                      debug=getOption("oceDebug"), monitor=FALSE, processingLog=NULL)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     type <- match.arg(type)
     ## FIXME: all these read.adv variants should have the same argument list
     if (type == "nortek")

R/adv.nortek.R

@@ -18,6 +18,8 @@ read.adv.nortek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                             haveAnalog1=FALSE, haveAnalog2=FALSE,
                             debug=getOption("oceDebug"), monitor=FALSE, processingLog=NULL)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ##   vvd=vector velocity data [p35 SIG], containing the data: pressure, vel, amp, corr (plus sensemble counter etc)
     ##   vsd=velocity system data [p36 SIG], containing times, temperatures, angles, etc
     ## NOTE: we interpolate from vsd to vvd, to get the final data$time, etc.

R/adv.sontek.R

@@ -8,6 +8,8 @@ read.adv.sontek.serial <- function(file, from=1, to, by=1, tz=getOption("oceTz")
                                    start=NULL, deltat=NULL,
                                    debug=getOption("oceDebug"), monitor=FALSE, processingLog=NULL)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, paste("read.adv.sontek.serial(file[1]=\"", file[1],
                            "\", from=", format(from),
                            if (!missing(to)) sprintf(", to=%s, ", format(to)),
@@ -154,6 +156,8 @@ read.adv.sontek.adr <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                                 longitude=NA, latitude=NA,
                                 debug=getOption("oceDebug"), monitor=FALSE, processingLog=NULL)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     bisectAdvSontekAdr <- function(burstTime, tFind, add=0, debug=0) {
         oceDebug(debug, "bisectAdvSontekAdr(tFind=", format(tFind), ", add=", add, "\n")
         len <- length(burstTime)
@@ -639,6 +643,8 @@ read.adv.sontek.text <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                                  debug=getOption("oceDebug"), monitor=FALSE,
                                  processingLog=NULL)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ## FIXME: It would be better to deal with the binary file, but the format is unclear to me;
     ## FIXME: two files are available to me, and they differ considerably, neither matching the
     ## FIXME: SonTek documentation.

R/amsr.R

@@ -562,6 +562,8 @@ download.amsr <- function(year, month, day, destdir=".", server="http://data.rem
 #' @md
 read.amsr <- function(file, debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.amsr(file=\"", file, "\",",
              #if (length(band) > 1) paste("band=c(\"", paste(band, collapse="\",\""), "\")", sep="") else
                  ", debug=", debug, ") {\n", sep="", unindent=1)

R/argo.R

@@ -1026,6 +1026,8 @@ argoDecodeFlags <- function(f) # local function
 #' @md
 read.argo <- function(file, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (!requireNamespace("ncdf4", quietly=TRUE))
         stop('must install.packages("ncdf4") to read argo data')
     if (missing(processingLog)) processingLog <- paste(deparse(match.call()), sep="", collapse="")

R/bremen.R

@@ -192,6 +192,8 @@ findInHeaderBremen <- function(key, lines)
 #' @md
 read.bremen <- function(file)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (is.character(file)) {
         filename <- fullFilename(file)
         file <- file(file, "r")

R/cm.R

@@ -470,6 +470,8 @@ read.cm <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                     longitude=NA, latitude=NA,
                     debug=getOption("oceDebug"), monitor=FALSE, processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.cm(file=\"", file,
               "\", from=", format(from),
               ", to=", if (missing(to)) "(missing)" else format(to), ", by=", by, "type=", type, ", ...) {\n", sep="", unindent=1)

R/coastline.R

@@ -966,6 +966,8 @@ read.coastline <- function(file,
                            type=c("R", "S", "mapgen", "shapefile", "openstreetmap"),
                            debug=getOption("oceDebug"), monitor=FALSE, processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     type <- match.arg(type)
     oceDebug(debug, "read.coastline(file=\"", file, "\", type=\"", type, "\", ...) {\n", sep="", unindent=1)
     file <- fullFilename(file)
@@ -1086,6 +1088,8 @@ read.coastline <- function(file,
 read.coastline.shapefile <- function(file, lonlim=c(-180, 180), latlim=c(-90, 90),
                                      debug=getOption("oceDebug"), monitor=FALSE, processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.shapefile(file=\"", file, "\", ...) {\n", sep="", unindent=1)
     shapeTypeList <- c("nullshape",    # 0
                        "point",        # 1
@@ -1295,6 +1299,8 @@ read.coastline.shapefile <- function(file, lonlim=c(-180, 180), latlim=c(-90, 90
 read.coastline.openstreetmap <- function(file, lonlim=c(-180, 180), latlim=c(-90, 90),
                                      debug=getOption("oceDebug"), monitor=FALSE, processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.coastline.openstreetmap(file=\"", file, "\", ...) {\n", sep="", unindent=1)
     ## FIXME: ignoring lonlim and latlim
     if (is.character(file)) {

R/ctd.R

@@ -4064,6 +4064,8 @@ plotScan <- function(x, which=1, xtype="scan", flipy=FALSE,
 read.ctd <- function(file, type=NULL, columns=NULL, station=NULL, missingValue, deploymentType="unknown",
                      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ## Special case: ruskin files are handled by read.rsk()
     if (is.character(file) && length(grep(".rsk$", file))) {
         return(read.rsk(file=file, debug=debug))

R/ctd.itp.R

@@ -20,6 +20,8 @@
 read.ctd.itp <- function(file, columns=NULL, station=NULL, missingValue, deploymentType="unknown",
                          monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.ctd.itp() {\n", unindent=1)
     if (is.character(file)) {
         filename <- fullFilename(file)

R/ctd.sbe.R

@@ -734,6 +734,8 @@ cnvName2oceName <- function(h, columns=NULL, debug=getOption("oceDebug"))
 read.ctd.sbe <- function(file, columns=NULL, station=NULL, missingValue, deploymentType="unknown",
                          monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (length(grep("\\*", file, ignore.case=TRUE))) {
         oceDebug(debug, "read.ctd.sbe(file=\"", file, "\") { # will read a series of files\n", unindent=1)
         files <- list.files(pattern=file)

R/ctd.woce.R

@@ -258,6 +258,8 @@ woceUnit2oceUnit <- function(woceUnit)
 read.ctd.woce <- function(file, columns=NULL, station=NULL, missingValue, deploymentType="unknown",
                           monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (length(grep("\\*", file))) {
         oceDebug(debug, "read.ctd.woce(file=\"", file, "\") { # will read a series of files\n", unindent=1)
         files <- list.files(pattern=file)
@@ -668,6 +670,8 @@ read.ctd.woce <- function(file, columns=NULL, station=NULL, missingValue, deploy
 read.ctd.woce.other <- function(file, columns=NULL, station=NULL, missingValue, deploymentType="unknown",
                                 monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ##EXPOCODE 06MT18/1      WHP-ID A1E    DATE 090591
     ##STNNBR    558 CASTNO   1 NO.RECORDS=   83
     ##INSTRUMENT NO. NB3 SAMPLING RATE  31.25 HZ

R/echosounder.R

@@ -830,6 +830,8 @@ read.echosounder <- function(file, channel=1, soundSpeed,
                              tz=getOption("oceTz"), debug=getOption("oceDebug"),
                              processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.echosounder(file=\"", file, "\", tz=\"", tz, "\", debug=", debug, ") {\n", sep="", unindent=1)
     ##ofile <- file
     filename <- NULL

R/g1sst.R

@@ -96,7 +96,7 @@ setMethod(f="[[<-",
 #' consulting reference 2 (clicking and unclicking the radio button to
 #' show just the data) that the field mostly derives from simulation.
 #'
-#' @param filename name of a netcdf file containing G1SST data.
+#' @param file character value containing the name of a netcdf file containing G1SST data.
 #'
 #' @return A [g1sst-class] object.
 #'
@@ -132,12 +132,16 @@ setMethod(f="[[<-",
 #' @family things related to satellite data
 #'
 #' @md
-read.g1sst <- function(filename)
+read.g1sst <- function(file)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (!requireNamespace("ncdf4", quietly=TRUE))
         stop('must install.packages("ncdf4") to read g1sst data')
-    f <- ncdf4::nc_open(filename)
-    res <- new("g1sst", filename=filename)
+    if (!is.character(file))
+        stop("file must be a character string")
+    f <- ncdf4::nc_open(file)
+    res <- new("g1sst", file=file)
     ## Change the 1-col ncdf4 output to a vector
     res@metadata$longitude <- as.vector(ncdf4::ncvar_get(f, "longitude"))
     res@metadata$latitude <- as.vector(ncdf4::ncvar_get(f, "latitude"))

R/gps.R

@@ -476,6 +476,8 @@ as.gps <- function(longitude, latitude, filename="")
 #' @md
 read.gps <- function(file, type=NULL, debug=getOption("oceDebug"), processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.gps(...) {\n", sep="", unindent=1)
     filename <- NULL
     if (is.character(file)) {

R/index.R

@@ -64,6 +64,8 @@
 #' @md
 read.index <- function(file, format, missingValue, tz=getOption("oceTz"), debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (is.character(file)) {
         ##filename <- fullFilename(file)
         file <- file(file, "r")

R/landsat.R

@@ -1086,6 +1086,8 @@ read.landsatmeta <- function(file, debug=getOption("oceDebug"))
 #' @md
 read.landsat <- function(file, band="all", emissivity=0.984, decimate, debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.landsat(file=\"", file, "\",",
              if (length(band) > 1) paste("band=c(\"", paste(band, collapse="\",\""), "\")", sep="") else
                  paste("band=\"", band, "\"", sep=""),

R/lisst.R

@@ -340,6 +340,8 @@ as.lisst <- function(data, filename="", year=0, tz="UTC", longitude=NA, latitude
 #' @md
 read.lisst <- function(file, year=0, tz="UTC", longitude=NA, latitude=NA)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     filename <- NULL
     if (is.character(file)) {
         filename <- fullFilename(file)

R/lobo.R

@@ -378,6 +378,8 @@ setMethod(f="plot",
 #' @family things related to lobo data
 read.lobo <- function(file, cols=7, processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     ## header <- scan(file, what=character(), sep="\t", nlines=1, quiet=TRUE)
     ## d <- scan(file, what=character(), sep="\t", skip=1,  quiet=TRUE)
     filename <- ""

R/met.R

@@ -557,6 +557,8 @@ metNames2oceNames <- function(names, scheme)
 #' @md
 read.met <- function(file, type=NULL, skip, tz=getOption("oceTz"), debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.met() {\n", unindent=1)
     if (is.character(file)) {
         filename <- fullFilename(file)

R/misc.R

@@ -282,6 +282,8 @@ argShow <- function(x, nshow=4, last=FALSE, sep="=")
 #'}
 read.woa <- function(file, name, positive=FALSE)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (!is.character(file))
         stop("'file' must be a character string")
     con <- ncdf4::nc_open(file)

R/oce.R

@@ -1990,6 +1990,8 @@ oceMagic <- function(file, debug=getOption("oceDebug"))
 #' plotTS(x) # just the TS
 read.oce <- function(file, ...)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     type <- oceMagic(file)
     dots <- list(...)
     debug <- if ("debug" %in% names(dots)) dots$debug else 0

R/odf.R

@@ -974,6 +974,8 @@ ODFListFromHeader <- function(header)
 #' @md
 read.odf <- function(file, columns=NULL, header="list", debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.odf(\"", file, "\", ...) {\n", unindent=1, sep="")
     if (!is.null(header)) {
         if (!is.character(header))

R/rsk.R

@@ -650,6 +650,8 @@ setMethod(f="plot",
 read.rsk <- function(file, from=1, to, by=1, type, tz=getOption("oceTz", default="UTC"),
                         patm=FALSE, processingLog, debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     debug <- max(0, min(debug, 2))
     oceDebug(debug, "read.rsk(file=\"", file, "\", from=", format(from),
              ", to=", if (missing(to))"(not given)" else format(to),

R/sealevel.R

@@ -694,6 +694,8 @@ setMethod(f="plot",
 #' @md
 read.sealevel <- function(file, tz=getOption("oceTz"), processingLog, debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     if (!is.character(file))
         stop("'file' must be a character string")
     fileOrig <- file

R/section.R

@@ -2082,6 +2082,8 @@ read.section <- function(file, directory, sectionId="", flags,
                          missingValue=-999,
                          debug=getOption("oceDebug"), processingLog)
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.section(file=\"", file, "\", ...) {\n", unindent=1)
     if (!missing(directory)) {
         if (!missing(file))

R/topo.R

@@ -856,6 +856,8 @@ setMethod(f="plot",
 #' @md
 read.topo <- function(file, debug=getOption("oceDebug"))
 {
+    if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
+        stop("empty file")
     oceDebug(debug, "read.topo(file=\"", file, "\") {\n", sep="", unindent=1)
     ## handle GEBCO netcdf files or an ascii format
     dataNamesOriginal <- list()