From c04846f086c62206c0b6dfb2f71664e0a4b15658 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Sun, 9 Apr 2017 18:04:44 +0200 Subject: [PATCH 1/6] Bug in nc2a, not dropping var_dim. --- R/NcToArray.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/NcToArray.R b/R/NcToArray.R index 45c3289..1945ff7 100644 --- a/R/NcToArray.R +++ b/R/NcToArray.R @@ -246,7 +246,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL, #names(dim(var_result)) <- sapply(file_object$var[[var_name]]$dim, '[[', 'name') } if (!is.null(var_result)) { - if (!drop_var_dim || (length(vars_to_read_vector) == 1)) { + if (!(drop_var_dim && (length(vars_to_read_vector) == 1))) { dim(var_result) <- c(setNames(1, var_tag), dim(var_result)) } attr(var_result, 'variables') <- structure(list(atts), .Names = var_name) -- GitLab From ded36c38e462a49acdd7c5f21e0e05873c04194d Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Sun, 9 Apr 2017 18:58:49 +0200 Subject: [PATCH 2/6] Doc enhancement. --- man/NcToArray.Rd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/man/NcToArray.Rd b/man/NcToArray.Rd index 855d344..ec48517 100644 --- a/man/NcToArray.Rd +++ b/man/NcToArray.Rd @@ -5,7 +5,7 @@ Read a NetCDF File Into an R Array } \description{ -Reads one or a set of variables together with metadata items from a NetCDF file into an R array. Indices to retrieve (not necessarily consecutive) can be specified for each of the dimensions. Depending on the format of the request, the variables will be merged in into a single extended array or returned in a list with an array for each variable. The different variables in the file are considered to be stored along a dimension called 'var', so reading a variable 'foo' with dimensions 'lat' and 'lon' would result in an array with the dimensions c('var' = 1, 'lat' = n_lats, 'lon' = n_lons). +Reads one or a set of variables together with metadata items from a single NetCDF file into an R array (see package 'startR' to read data from multiple files/data sets). Indices to retrieve (not necessarily consecutive) can be specified for each of the dimensions. Depending on the format of the request, the variables will be merged in into a single extended array or returned in a list with an array for each variable. The different variables in the file are considered to be stored along a dimension called 'var', so reading a variable 'foo' with dimensions 'lat' and 'lon' would result in an array with the dimensions c('var' = 1, 'lat' = n_lats, 'lon' = n_lons). } \usage{ NcToArray(file_to_read, dim_indices = NULL, vars_to_read = NULL, @@ -17,7 +17,7 @@ nc2a(file_to_read, dim_indices = NULL, vars_to_read = NULL, } \arguments{ \item{file_to_read}{ -Path to the file to be read or a NetCDF object as returned by \code{easyNCDF::NcOpen} or \code{ncdf4::nc_open}. +Path to the file to be read or a NetCDF object as returned by \code{easyNCDF::NcOpen} or \code{ncdf4::nc_open}. See package 'startR' if need to read data from multiple files/data sets. } \item{dim_indices}{ Named list with numeric vectors of indices to take for each dimension. The names should correspond to the dimension names which to take the indices for. Non-consecutive indices can be specified. If \code{expect_all_indices = FALSE} (default), it is not mandatory to specify the indices for all (or even any of) the dimensions. In that case all the indices along such dimensions will be read in. If \code{expect_all_indices = TRUE}, then indices for all the dimensions have to be specified for the function to return a data array. In that case, \code{NA} can be used to request all indices for a dimension if desired. -- GitLab From 8a48c79e5e3e871849c5270342dff28c0f7dcb2d Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Tue, 11 Apr 2017 19:56:35 +0200 Subject: [PATCH 3/6] Minor fixes. --- R/NcToArray.R | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/R/NcToArray.R b/R/NcToArray.R index 1945ff7..30561c0 100644 --- a/R/NcToArray.R +++ b/R/NcToArray.R @@ -72,7 +72,6 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL, # if (!is.character(vars_to_read) && !is.numeric(vars_to_read)) { # stop("Parameter 'vars_to_read' must be a numeric vector or vector of character strings.") # } - result_list <- NULL for (vars_to_read_vector in vars_to_read) { result <- NULL @@ -94,12 +93,11 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL, } #file_object$var[extra_dimvars] <- extra_dimvars_list #file_object$nvars <- file_object$nvars + length(extra_dimvars) - nmv <- numeric_var_indices <- which(is.numeric(vars_to_read_vector)) - if (length(nmv) > 0) { - if (any(vars_to_read_vector[nmv] > (length(file_object$var) + length(extra_dimvars)))) { + if (is.numeric(vars_to_read_vector)) { + if (any(vars_to_read_vector > (length(file_object$var) + length(extra_dimvars)))) { stop("Provided numerical variable indices out of bounds in 'vars_to_read'.") } - vars_to_read_vector[nmv] <- c(sapply(file_object$var, '[[', 'name'), extra_dimvars)[vars_to_read_vector[nmv]] + vars_to_read_vector <- c(sapply(file_object$var, '[[', 'name'), extra_dimvars)[vars_to_read_vector] } for (var_name in vars_to_read_vector) { if (var_name %in% extra_dimvars) { -- GitLab From 482a523a7f7bdf53117dc5ae5e1a2d2f25645ec5 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Thu, 13 Apr 2017 02:32:20 +0200 Subject: [PATCH 4/6] Fixes to support character variables. --- R/NcReadDims.R | 5 + R/NcToArray.R | 13 ++ R/Utils.R | 319 +++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 337 insertions(+) diff --git a/R/NcReadDims.R b/R/NcReadDims.R index ce4a095..660b4ef 100644 --- a/R/NcReadDims.R +++ b/R/NcReadDims.R @@ -44,6 +44,11 @@ NcReadDims <- function(file_to_read, var_names = NULL) { } found_dims <- file_object$var[[var_name]]$size names(found_dims) <- sapply(file_object$var[[var_name]]$dim, '[[', 'name') + # Support for character strings + if ((file_object$var[[var_name]]$prec == 'char') && + (length(file_object$var[[var_name]][['dim']]) > 1)) { + found_dims <- found_dims[-1] + } new_dim <- c(var = 1) found_dims <- c(new_dim, found_dims) if (!is.null(dims)) { diff --git a/R/NcToArray.R b/R/NcToArray.R index 30561c0..27b7099 100644 --- a/R/NcToArray.R +++ b/R/NcToArray.R @@ -212,8 +212,21 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL, } start <- sapply(indices_to_take, function(x) if (is_single_na(x)) 1 else min(x)) count <- sapply(indices_to_take, function(x) if (is_single_na(x)) -1 else max(x) - min(x) + 1) + # Support for character strings + if ((file_object[['var']][[var_name]][['prec']] == 'char') && + (length(file_object[['var']][[var_name]][['dim']]) > 1)) { + start <- c(1, start) + count <- c(-1, count) + original_ncvar_get_inner <- ncdf4:::ncvar_get_inner + assignInNamespace('ncvar_get_inner', .ncvar_get_inner, 'ncdf4') + } var_result <- do.call('[', c(list(ncvar_get(file_object, var_name, start, count, collapse_degen = FALSE)), lapply(indices_to_take, function(x) if (is_single_na(x)) TRUE else x - min(x) + 1), list(drop = FALSE))) + # Support for character strings + if ((file_object[['var']][[var_name]][['prec']] == 'char') && + (length(file_object[['var']][[var_name]][['dim']]) > 1)) { + assignInNamespace('ncvar_get_inner', original_ncvar_get_inner, 'ncdf4') + } #metadata <- c(metadata, structure(list(file_object$var[[var_name]]), .Names = var_name)) ## TODO: Crop dimensions in attributes if (!is.null(reorder_back)) { diff --git a/R/Utils.R b/R/Utils.R index 82c2fb6..27be8dd 100644 --- a/R/Utils.R +++ b/R/Utils.R @@ -203,3 +203,322 @@ names(dim(array1)) <- names(dim(array2)) array1 } + +# This function is a copy of the function ncvar_get_inner in 'ncdf4' package +# with a bugfix. When ncdf4 addresses this bug, this function will be removed +# from this package. +.ncvar_get_inner <- function( ncid, varid, missval, addOffset=0., scaleFact=1.0, start=NA, count=NA, verbose=FALSE, signedbyte=TRUE, + collapse_degen=TRUE, raw_datavals=FALSE ) { + + if( ! is.numeric(ncid)) + stop("Error, first arg passed to ncvar_get_inner (ncid) must be a simple C-style integer that is passed directly to the C api") + if( ! is.numeric(varid)) + + stop("Error, second arg passed to ncvar_get_inner (varid) must be a simple C-style integer that is passed directly to the C api") + + if( verbose ) { + print(paste("ncvar_get_inner: entering with (C-STYLE INTEGER ONLY) ncid=", ncid, + "varid=", varid )) + print(paste("ncvar_get_inner: following line is collapse_degen:")) + print(collapse_degen) + } + + tmp_typename = c('short', 'int', 'float', 'double', 'char', 'byte' ) + + have_start = (length(start)>1) || ((length(start)==1) && (!is.na(start))) + have_count = (length(count)>1) || ((length(count)==1) && (!is.na(count))) + + sm <- storage.mode(start) + if( (sm != "double") && (sm != "integer") && (sm != "logical")) + stop(paste("passed a start argument of storage mode",sm,"; can only handle double or integer")) + sm <- storage.mode(count) + if( (sm != "double") && (sm != "integer") && (sm != "logical")) + stop(paste("passed a 'count' argument with storage mode '",sm,"'; can only handle double or integer", sep='')) + + if( signedbyte ) + byte_style = 1 # 1=signed + else + byte_style = 2 # 2=unsigned + + varsize <- ncdf4:::ncvar_size ( ncid, varid ) + ndims <- ncdf4:::ncvar_ndims( ncid, varid ) + if( verbose ) { + print(paste("ndims:",ndims)) + print("ncvar_get: varsize:") + print(varsize) + } + + #------------------------------ + # Fix up start and count to use + #------------------------------ + if( ndims == 0 ) { + start <- 1 + count <- 1 + } + else + { + if( ! have_start ) + start <- rep(1,ndims) # Note: use R convention for now + if( ! have_count ) + count <- varsize - start + 1 + else + { + #------------------ + # Take care of -1's + #------------------ + count <- ifelse( (count == -1), varsize-start+1, count) + } + } + if( verbose ) { + print("ncvar_get: start:") + print(start) + print("ncvar_get: count:") + print(count) + } + + if( ndims > 0 ) { + if( length(start) != ndims ) + stop(paste("Error: variable has",ndims,"dims, but start has",length(start),"entries. They must match!")) + if( length(count) != ndims ) + stop(paste("Error: variable has",ndims,"dims, but count has",length(count),"entries. They must match!")) + } + + #---------------------------------------- + # Need to know how much space to allocate + #---------------------------------------- + totvarsize <- prod(count) + if( verbose ) + print(paste("ncvar_get: totvarsize:",totvarsize)) + + #-------------------------------------------------- + # Switch from R to C convention for start and count + #-------------------------------------------------- + c.start <- start[ ndims:1 ] - 1 + c.count <- count[ ndims:1 ] + + rv <- list() + rv$error <- -1 + + #--------------------------------- + # Get the correct type of variable + #--------------------------------- + precint <- ncdf4:::ncvar_type( ncid, varid ) # 1=short, 2=int, 3=float, 4=double, 5=char, 6=byte, 7=ubyte, 8=ushort, 9=uint, 10=int64, 11=uint64, 12=string + if( verbose ) + print(paste("ncvar_get_inner: getting var of type",tmp_typename[precint], 'id=', precint)) + + if( (precint == 1) || (precint == 2) || (precint == 6) || (precint == 7) || (precint == 8)) { + #-------------------------------- + # Short, Int, Byte, UByte, UShort + #-------------------------------- + rv <- .Call("Rsx_nc4_get_vara_int", + as.integer(ncid), + as.integer(varid), + as.integer(c.start), # Already switched to C convention... + as.integer(c.count), # Already switched to C convention... + as.integer(byte_style), # 1=signed, 2=unsigned + PACKAGE="ncdf4") + if( rv$error != 0 ) + stop("C function Rsx_nc4_get_var_int returned error") + data = rv$data + } + + else if( (precint == 3) || (precint == 4)) { + #---------------------------------------------------------------- + # Float, double where we have the C routine fix the missing value + # 'imvstate' is: 0 if we do not have a missing value (it is NULL), + # 1 if the missing value is NA, 2 if the missing value is present + # and not NULL and not NA. These codes are used by the C routine + #---------------------------------------------------------------- + if( is.null( missval )) { + passed_missval = 0.0 + imvstate = as.integer(0) + } + else if( is.na(missval)) { + passed_missval = 0.0 + imvstate = as.integer(1) + } + else + { + passed_missval = missval + imvstate = as.integer(2) + } + + if( raw_datavals ) + fixmiss = as.integer(0) # setting 'raw_datavalues' to TRUE gives the actual raw numbers from the file, not processed at all + else + fixmiss = as.integer(1) + + if( verbose ) print('about to call Rsx_nc4_get_vara_double...') + rv <- .Call("Rsx_nc4_get_vara_double", + as.integer(ncid), + as.integer(varid), + as.integer(c.start), # Already switched to C convention... + as.integer(c.count), # Already switched to C convention... + fixmiss, + imvstate, + as.double(passed_missval), + PACKAGE="ncdf4") + if( rv$error != 0 ) + stop("C function R_nc4_get_vara_double returned error") + if( verbose ) print('back from call to Rsx_nc4_get_vara_double...') + data = rv$data + } + + else if( (precint == 9) || (precint == 10) || (precint == 11)) { + #--------------------------------------------- + # uint, int64, uint64 + # Thanks to Tom Hilinski of Colorado State for + # fix to uint here + #--------------------------------------------- + rv$data <- double(totvarsize) + fixmiss = as.integer(0) + rv <- .Call("Rsx_nc4_get_vara_double", + as.integer(ncid), + as.integer(varid), + as.integer(c.start), # Already switched to C convention... + as.integer(c.count), # Already switched to C convention... + fixmiss, + as.integer(-1), # The 'imvstate' arg is unused in this call since no fixmiss + as.double(0.0), # the passed missing value is not used in this call since no fixmiss + PACKAGE="ncdf4") + if( rv$error != 0 ) + stop("C function R_nc4_get_vara_double returned error") + data = rv$data + } + + else if( precint == 5 ) { + #----- + # Char + #----- + strndims <- ndims - 1 + strlen <- count[1] + 1 + strdim <- 1 + if( strndims >= 1 ) { + strdim <- count[2:ndims] + nstr <- prod(strdim) + } + else + nstr <- 1 + if(verbose) + print(paste("ndims:",ndims,"strndims:",strndims,"strlen:",strlen,"nstr:",nstr)) + + #---------------------------------------------- + # Make a character string of the specified size + #---------------------------------------------- + stor <- ncdf4:::blankstring_ncdf4( totvarsize ) + stordata <- ncdf4:::blankstring_ncdf4(strlen) + if( verbose ) + print(paste("length of stor string:",nchar(stor))) + rv$tempstore <- stor + rv$data <- array(stordata, dim=strdim) + + rv <- .C("R_nc4_get_vara_text", + as.integer(ncid), + as.integer(varid), + as.integer(c.start), # Already switched to C convention... + as.integer(c.count), # Already switched to C convention... + tempstore=as.character(rv$tempstore), + data=as.character(rv$data), + error=as.integer(rv$error), + PACKAGE="ncdf4") + if( rv$error != 0 ) + stop("C function R_nc4_get_var_text returned error") + + dim(rv$data) <- strdim + } + + else if( precint == 12 ) { + #----------------------------- + # netcdf version 4 String type + #----------------------------- + rv <- .Call( "R_nc4_get_vara_string", + as.integer(ncid), + as.integer(varid), + as.integer(c.start), # Already switched to C convention... + as.integer(c.count), # Already switched to C convention... + PACKAGE="ncdf4" ) + } + else + { + stop(paste("Trying to get variable of an unhandled type code: ",precint, "(", ncdf4:::ncvar_type_to_string(precint), ")")) + } + if( verbose ) { + print(paste("ncvar_get_inner: C call returned",rv$error)) + print(paste("ncvar_get_inner: dim of directly returned array:")) + print(dim(rv$data)) + } + + #-------------------------------------------------------- + # Set our dims...but collapse degenerate dimensions first + #-------------------------------------------------------- + if( ndims > 0 ) { + if( collapse_degen ) { + count.nodegen <- vector() + foundone <- 0 + for( i in 1:ndims ) + if( count[i] > 1 ) { + count.nodegen <- append(count.nodegen, count[i]) + foundone <- 1 + } + if( foundone == 0 ) + dim(rv$data) <- (1) + else + { + if( verbose ) + print(paste("count.nodegen:",count.nodegen," Length of data:",length(rv$data))) + if( precint != 5 ) + dim(rv$data) <- count.nodegen + } + } + else if (precint != 5) + dim(rv$data) = count + + if( verbose ) { + print("ncvar_get: final dims of returned array:") + print(dim(rv$data)) + } + } + + #---------------------------------------------------------- + # Change missing values to "NA"s. Note that 'varid2Rindex' + # is NOT filled out for dimvars, so skip this if a dimvar + # 1=short, 2=int, 3=float, 4=double, 5=char, 6=byte + # NOTE: if type is 3 or 4 (float or double), the missing + # value was already set by the C routine. + #---------------------------------------------------------- + if( (!raw_datavals) && (precint != 5) && (precint != 3) && (precint != 4) ) { # not char, float, or double + if( verbose ) print("ncvar_get: setting missing values to NA") + if( (precint==1) || (precint==2) || (precint==6) || (precint==7) || (precint==8) || (precint==9)) { + #-------------------------------------- + # Short, Int, Byte, UByte, UShort, UInt + #-------------------------------------- + if( verbose ) print(paste("ncvar_get_inner: setting ", tmp_typename[precint],"-type missing value of ", missval, " to NA", sep='')) + if( ! is.na(missval) ) + rv$data[rv$data==missval] <- NA + } + else if( (precint==10) || (precint==11)) { + #-------------------------------- + # 8-byte int, unsigned 8-byte int + #-------------------------------- + if( ! is.na(missval) ) { + tol <- abs(missval*1.e-5) + if( verbose ) print(paste("ncvar_get_inner: setting ", tmp_typename[precint],"-type missing value of ", missval, + " (w/tolerance ", tol,") to NA", sep='')) + rv$data[abs(rv$data-missval)= 2.14.1) @@ -15,3 +16,4 @@ URL: https://earth.bsc.es/gitlab/es/easyNCDF/wikis/home BugReports: https://earth.bsc.es/gitlab/es/easyNCDF/issues LazyData: true SystemRequirements: netcdf development libraries +NeedsCompilation: yes diff --git a/NAMESPACE b/NAMESPACE index 9baf4ba..de2ea64 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,3 +1,4 @@ +useDynLib(easyNCDF) exportPattern("^[^\\.]") import(ncdf4, abind) importFrom("stats", "setNames") diff --git a/R/NcToArray.R b/R/NcToArray.R index cda45d2..af82c57 100644 --- a/R/NcToArray.R +++ b/R/NcToArray.R @@ -203,16 +203,16 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL, (length(file_object[['var']][[var_name]][['dim']]) > 1)) { start <- c(1, start) count <- c(-1, count) - original_ncvar_get_inner <- ncdf4:::ncvar_get_inner - assignInNamespace('ncvar_get_inner', .ncvar_get_inner, 'ncdf4') + ##original_ncvar_get_inner <- ncdf4:::ncvar_get_inner + ##assignInNamespace('ncvar_get_inner', .ncvar_get_inner, 'ncdf4') } - var_result <- do.call('[', c(list(ncvar_get(file_object, var_name, start, count, collapse_degen = FALSE)), + var_result <- do.call('[', c(list(.ncvar_get(file_object, var_name, start, count, collapse_degen = FALSE)), lapply(indices_to_take, function(x) if (is_single_na(x)) TRUE else x - min(x) + 1), list(drop = FALSE))) - # Support for character strings - if ((file_object[['var']][[var_name]][['prec']] == 'char') && - (length(file_object[['var']][[var_name]][['dim']]) > 1)) { - assignInNamespace('ncvar_get_inner', original_ncvar_get_inner, 'ncdf4') - } + ### Support for character strings + ##if ((file_object[['var']][[var_name]][['prec']] == 'char') && + ## (length(file_object[['var']][[var_name]][['dim']]) > 1)) { + ## assignInNamespace('ncvar_get_inner', original_ncvar_get_inner, 'ncdf4') + ##} #metadata <- c(metadata, structure(list(file_object$var[[var_name]]), .Names = var_name)) names(dim(var_result)) <- names(indices_to_take) # Drop extra dims diff --git a/R/Utils.R b/R/Utils.R index 27be8dd..5cd9374 100644 --- a/R/Utils.R +++ b/R/Utils.R @@ -204,9 +204,128 @@ array1 } -# This function is a copy of the function ncvar_get_inner in 'ncdf4' package -# with a bugfix. When ncdf4 addresses this bug, this function will be removed -# from this package. +# The functions from here on are copies of some functions in 'ncdf4' package +# with a small bugfix in ncvar_get_inner. When ncdf4 addresses this bug, these +# function will be removed from this package. +# This code belongs to David Pierce. +.ncvar_size <- function( ncid, varid ) { + + if( mode(ncid) != 'numeric' ) + stop(paste("error, must be passed a numeric first arg: ncid2use, not an arg of mode", mode(ncid))) + + if( mode(varid) != 'numeric' ) + stop("Error, must be passed a numeric second arg: varid2use" ) + + ndims <- .ncvar_ndims( ncid, varid ) + if( ndims == 0 ) + #return(vector()) changed DWP 2012-09-20 + return(1) # indicates a scalar var + + rv <- list() + rv$error <- -1 + rv$varsize <- integer(ndims) + rv$ndims <- -1 + rv <- .C("R_nc4_varsize", + as.integer(ncid), + as.integer(varid), + ndims=as.integer(rv$ndims), + varsize=as.integer(rv$varsize), + error=as.integer(rv$error), + PACKAGE="easyNCDF") + if( rv$error != 0 ) + stop("error returned from C routine R_nc4_varsize") + + #------------------------------------- + # Switch order from C-style to R-style + #------------------------------------- + rv$varsize <- rv$varsize[ ndims:1 ] + + return(rv$varsize) +} + +.ncvar_type <- function( ncid, varid, output_string=FALSE ) { + + if( mode(ncid) != 'numeric' ) + stop("error, must be passed a numeric first arg: ncid2use") + + if( mode(varid) != 'numeric' ) + stop("Error, must be passed a numeric second arg: varid2use" ) + + rv <- list() + rv$error <- -1 + rv$precint <- -1 + + rv <- .C("R_nc4_inq_vartype", + as.integer(ncid), + as.integer(varid), + precint=as.integer(rv$precint), + error=as.integer(rv$error), + PACKAGE="easyNCDF") + if( rv$error != 0 ) + stop("error returned from C call") + return( rv$precint ) +} + +.ncvar_ndims <- function( ncid, varid ) { + + if( mode(ncid) != 'numeric' ) + stop(paste("error, ncvar_ndims must be passed a numeric first arg; mode of val passed=", mode(ncid))) + + if( mode(varid) != 'numeric' ) + stop("Error, ncvar_ndims must be passed a numeric second arg: varid2use" ) + + rv <- list() + rv$error <- -1 + rv$ndims <- -1 + rv <- .C("R_nc4_inq_varndims", + as.integer(ncid), + as.integer(varid), + ndims=as.integer(rv$ndims), + error=as.integer(rv$error), + PACKAGE="easyNCDF") + if( rv$error != 0 ) + stop("error returned from C call") + return( rv$ndims ) +} + +.blankstring_ncdf4 <- function( n ) { + + rv <- .Call("R_nc4_blankstring", as.integer(n), PACKAGE="easyNCDF") + return( rv ) +} + +.ncvar_type_to_string <- function( precint ) { + + if( precint == 1 ) + prec <- "short" + else if( precint == 2 ) + prec <- "int" + else if( precint == 3 ) + prec <- "float" + else if( precint == 4 ) + prec <- "double" + else if( precint == 5 ) + prec <- "char" + else if( precint == 6 ) + prec <- "byte" + else if( precint == 7 ) + prec <- "unsigned byte" + else if( precint == 8 ) + prec <- "unsigned short" + else if( precint == 9 ) + prec <- "unsigned int" + else if( precint == 10 ) + prec <- "8 byte int" + else if( precint == 11 ) + prec <- "unsinged 8 byte int" + else if( precint == 12 ) + prec <- "string" + else + stop(paste("Error, unrecognized type code of variable supplied:", precint )) + + return( prec ) +} + .ncvar_get_inner <- function( ncid, varid, missval, addOffset=0., scaleFact=1.0, start=NA, count=NA, verbose=FALSE, signedbyte=TRUE, collapse_degen=TRUE, raw_datavals=FALSE ) { @@ -240,8 +359,8 @@ else byte_style = 2 # 2=unsigned - varsize <- ncdf4:::ncvar_size ( ncid, varid ) - ndims <- ncdf4:::ncvar_ndims( ncid, varid ) + varsize <- .ncvar_size ( ncid, varid ) + ndims <- .ncvar_ndims( ncid, varid ) if( verbose ) { print(paste("ndims:",ndims)) print("ncvar_get: varsize:") @@ -302,7 +421,7 @@ #--------------------------------- # Get the correct type of variable #--------------------------------- - precint <- ncdf4:::ncvar_type( ncid, varid ) # 1=short, 2=int, 3=float, 4=double, 5=char, 6=byte, 7=ubyte, 8=ushort, 9=uint, 10=int64, 11=uint64, 12=string + precint <- .ncvar_type( ncid, varid ) # 1=short, 2=int, 3=float, 4=double, 5=char, 6=byte, 7=ubyte, 8=ushort, 9=uint, 10=int64, 11=uint64, 12=string if( verbose ) print(paste("ncvar_get_inner: getting var of type",tmp_typename[precint], 'id=', precint)) @@ -316,7 +435,7 @@ as.integer(c.start), # Already switched to C convention... as.integer(c.count), # Already switched to C convention... as.integer(byte_style), # 1=signed, 2=unsigned - PACKAGE="ncdf4") + PACKAGE="easyNCDF") if( rv$error != 0 ) stop("C function Rsx_nc4_get_var_int returned error") data = rv$data @@ -357,7 +476,7 @@ fixmiss, imvstate, as.double(passed_missval), - PACKAGE="ncdf4") + PACKAGE="easyNCDF") if( rv$error != 0 ) stop("C function R_nc4_get_vara_double returned error") if( verbose ) print('back from call to Rsx_nc4_get_vara_double...') @@ -380,7 +499,7 @@ fixmiss, as.integer(-1), # The 'imvstate' arg is unused in this call since no fixmiss as.double(0.0), # the passed missing value is not used in this call since no fixmiss - PACKAGE="ncdf4") + PACKAGE="easyNCDF") if( rv$error != 0 ) stop("C function R_nc4_get_vara_double returned error") data = rv$data @@ -405,8 +524,8 @@ #---------------------------------------------- # Make a character string of the specified size #---------------------------------------------- - stor <- ncdf4:::blankstring_ncdf4( totvarsize ) - stordata <- ncdf4:::blankstring_ncdf4(strlen) + stor <- .blankstring_ncdf4( totvarsize ) + stordata <- .blankstring_ncdf4(strlen) if( verbose ) print(paste("length of stor string:",nchar(stor))) rv$tempstore <- stor @@ -420,7 +539,7 @@ tempstore=as.character(rv$tempstore), data=as.character(rv$data), error=as.integer(rv$error), - PACKAGE="ncdf4") + PACKAGE="easyNCDF") if( rv$error != 0 ) stop("C function R_nc4_get_var_text returned error") @@ -436,11 +555,11 @@ as.integer(varid), as.integer(c.start), # Already switched to C convention... as.integer(c.count), # Already switched to C convention... - PACKAGE="ncdf4" ) + PACKAGE="easyNCDF" ) } else { - stop(paste("Trying to get variable of an unhandled type code: ",precint, "(", ncdf4:::ncvar_type_to_string(precint), ")")) + stop(paste("Trying to get variable of an unhandled type code: ",precint, "(", .ncvar_type_to_string(precint), ")")) } if( verbose ) { print(paste("ncvar_get_inner: C call returned",rv$error)) @@ -522,3 +641,442 @@ return(rv$data) } + +.ncdf4_inner_open <- function( nc ) { + + if( class( nc ) != 'ncdf4' ) + stop(paste("ncdf4 library: internal error: ncdf4_inner_open called with an object that is NOT class ncdf4!")) + + rv <- list() + + if( is.null(nc$writable)) + stop(paste("Internal error: ncdf4_inner_open called with no $writable element on file", nc$filename)) + if( nc$writable ) + rv$cmode <- 1 + else + rv$cmode <- 0 + + rv$id <- -1 + rv$error <- -1 + rv <- .C("R_nc4_open", + as.character(nc$filename), + as.integer(rv$cmode), # write mode=1, read only=0 + id=as.integer(rv$id), # note: nc$id is the simple integer ncid of the base file (root group in the file) + error=as.integer(rv$error), + PACKAGE="easyNCDF") + if( rv$error != 0 ) + stop(paste("Error in nc_open trying to open file",nc$filename)) + + return( rv$id ) +} + +.ncdf4_make_id <- function( id=-1, group_index=-1, group_id=-1, list_index=-1, isdimvar=FALSE ) { + + retval <- list( id=id, group_index=group_index, group_id=group_id, + list_index=list_index, isdimvar=isdimvar ) + class(retval) <- 'ncid4' + return( retval ) +} + +.vobjtovarid4 <- function( nc, varid, verbose=FALSE, allowdimvar=TRUE) { + + if( verbose ) + print(paste("vobjtovarid4: entering")) + + if( class(nc) != 'ncdf4' ) + stop('First passed argument (nc) must be an object of class ncdf4, as returned by nc_open() or nc_create()') + + if( (class(varid) != 'ncvar4') && (class(varid) != 'ncdim4') && (class(varid) != 'ncid4') && (!is.character(varid)) && (!is.na(varid))) + stop('Second passed argument (varid) must be an object of class ncvar4 or ncid4, the character string name of a variable, or a NA (indicating to use the only var in the file)') + + #------------------------------------------------------------- + # Easiest case is if we were given a ncid object to begin with + #------------------------------------------------------------- + if( class(varid) == 'ncid4' ) { + if(verbose) print("vobjtovarid4: passed varid was an ncid, easy exit") + return( varid ) # an object of class 'ncid4', not a simple integer + } + + #------------------------------------------------------------ + # Handle case where we are given a ncvar object to begin with + #------------------------------------------------------------ + if( class(varid) == "ncvar4" ) { + + origvarid <- varid + if(verbose) + print(paste("vobjtovarid4: passed a ncvar class, name=",varid$name)) + varid <- nc$var[[varid$name]]$id # Note we do NOT use varid$id in case var is from different file (but names are same) + if( is.null(varid)) { + print('------------------------------------------------------') + print(paste("Error, var '", origvarid$name,"' was not found in file '", nc$filename, "'", sep='')) + print(paste('Hint: make SURE the variable was not only defined with a call to ncvar_def(), but also included in the list of variables passed to nc_create()')) + stop('stopping') + } + if( class(varid) != 'ncid4' ) { + print('------------------------------') + print("here is varid:") + print(varid) + stop(paste("Internal error #E, returned varid is not a object of class ncid4")) + } + + #----------------------------------------------------------------- + # Make sure this varid that will be returned has valid information + #----------------------------------------------------------------- + varidOK <- ((varid$id>=0) && (varid$id<=100000) && (varid$group_id >= 0)) + if( is.na(varidOK) || (!varidOK)) { + print("vobjtovarid4: I was passed a ncvar object, BUT this object does NOT refer to any valid var in the netcdf file!") + print(paste("This happened for netCDF filename:",nc$filename)) + print("Here are the vars in the netCDF file:") + for( ii in 1:nc$nvars ) + print(paste(ii,": ",nc$var[[ii]]$name, sep='' )) + print(paste("The passed varid object (which does NOT exist in that file) is:")) + print(origvarid) + print(paste("Hint: make SURE the variable was not only defined with a call to ncvar_def(), but also included in the list of variables passed to nc_create()")) + stop("stopping") + } + + if( verbose ) + print(paste("vobjtovarid4: returning with varid deduced from a passed ncvar object; varid=", + varid$group_id, varid$id)) + return(varid) # an object of class 'ncid4' + } + + #------------------------------------------------------------- + # Handle case where we are given an ncdim object to begin with + #------------------------------------------------------------- + if( class(varid) == "ncdim4" ) { + + if( ! allowdimvar ) + stop(paste("Error, I was NOT allowed to check dimvars, but the second argument passed was an object of class ncdim4! Name=", varid$name)) + + if(verbose) + print(paste("vobjtovarid4: passed a ncdim class, name=",varid$name)) + + #----------------------------------------------------------- + # Go through and find if there is a dim in the file that has + # the same name as this dim. We do not immediately use + # this dim's dimvarid in case the dim is from a different + # file but has the same name. + #----------------------------------------------------------- + name2find = varid$name + foundit = FALSE + for( idim in 1:nc$ndims ) { + if( nc$dim[[idim]]$name == name2find ) { + #------------------------------------------- + # Remember we return the DIMVAR, not the dim + #------------------------------------------- + retval = nc$dim[[idim]]$dimvarid # an object of type 'ncid' + foundit = TRUE + break + } + } + if( ! foundit ) + #----------------------------------------------------------- + # Return an ncid that indicates this is a dimvar but it does + # not exist in the file + #----------------------------------------------------------- + retval = .ncdf4_make_id( id=-1, group_index=-1, group_id=-1, list_index=-1, isdimvar=TRUE ) + + if( class(retval) != 'ncid4' ) + stop(paste("Internal error #C, returned varid is not a object of class ncid4. Case with ncdim object passed; ncdim name=", varid$name)) + + if( verbose ) + print(paste("vobjtovarid4: returning with varid deduced from a passed ncvar object; retval=", + retval$group_id, retval$id)) + return(retval) # an object of class 'ncid4' + } + + #---------------------------------------------------------- + # If we get here, 'varid' can be a NA or a character string + #---------------------------------------------------------- + + #--------------------------------------------------------------------------- + # If varid is NA, then return the only var in the file (if there IS only one + # var in the file). If there is more than one var in the file, return the + # one with the most dimensions, IF that highest-dimensionality var has more + # dimensions than any other var in the file. Otherwise, generate an error. + #--------------------------------------------------------------------------- + if( (length(varid)==1) && is.na(varid)) { + if( nc$nvars == 1 ) { + varToUse <- 1 + } + else + { + #------------------------------------------------------------ + # Choose the most complicated var, if there is one, otherwise + # halt with an error + #------------------------------------------------------------ + varToUse <- -1 + ndimsItHas <- -1 + for( ii in 1:nc$nvars ) { + if( nc$var[[ii]]$ndims > ndimsItHas ) { + varToUse <- ii + ndimsItHas <- nc$var[[ii]]$ndims + } + } + for( ii in 1:nc$nvars ) { + if( (ii != varToUse) && (nc$var[[ii]]$ndims == ndimsItHas)) { + stop(paste("File",nc$filename,"has more than one variable, so you must explicitly specify which one you want")) + } + } + } + varid <- nc$var[[varToUse]]$id # remember, an object of class 'ncid4', not a simple int + if( class(varid) != 'ncid4' ) + stop(paste("internal error #B, returned varid is not of class ncid4")) + + if( verbose ) + print(paste("vobjtovarid4: returning with only var in file; id=", + nc$var[[varToUse]]$id$group_id, nc$var[[varToUse]]$id$id)) + return( varid ) # an object of class 'ncid4' + } + + #--------------------------------------------------- + # If we get here, 'varid' must be a character string + #--------------------------------------------------- + if( ! is.character(varid)) + stop("internal error: location #M: varid is not a character string!") + + origvarid <- varid + + #------------------------------------------- + # Make sure var name follows our conventions + #------------------------------------------- + if( substr(varid,1,1) == '/' ) + stop(paste("Error, I was given a name that starts with a slash; fully qualified names NEVER start with a slash (this is required for backwards compatability). Leave off the leading slash!")) + + #-------------------------------------------- + # See if any vars in this file have this name + #-------------------------------------------- + varToUse <- -1 + if( nc$nvars > 0 ) { + for( kk in 1:nc$nvars ) { + if( origvarid == nc$var[[kk]]$name ) # check to see if fully qualified name matches + varToUse <- kk + } + } + + #--------------------------------- + # Found a var with the right name, + # return its ncid object + #--------------------------------- + if( varToUse != -1 ) { + if(verbose) + print(paste("Variable named",origvarid,"found in file with varid=", + nc$var[[varToUse]]$id$group_id, nc$var[[varToUse]]$id$id)) + varid <- nc$var[[varToUse]]$id # remember, an object of class 'ncid4', not a simple int + if( class(varid) != 'ncid4' ) { + print('---- varid:') + print(varid) + stop(paste("internal error #A, returned varid is not of class ncid4")) + } + return( varid ) # an object of class 'ncid4' + } + + #--------------------------------------------------------------- + # A var with this name was NOT found in the file. But, it could + # be the name of a dimvar in the file. Check to see if we are + # allowed to return dimvars in this case. + #--------------------------------------------------------------- + if( ! allowdimvar ) { + print("vobjtovarid4: error #G: I could not find the requested var in the file!") + print(paste("requested var name:",origvarid)) + print(paste("file name:",nc$filename)) + print("Note: I was NOT allowed to check to see if this was a dimvar name") + stop("Variable not found") + } + + if(verbose) + print(paste("Variable named",origvarid,"NOT found in file; looking for a dimvar with this name")) + + #----------------------------------------------- + # Check to see if passed name matches a dim name + #----------------------------------------------- + for( i in 1:nc$ndims ) { + if( origvarid == nc$dim[[i]]$name ) { + #--------------------- + # Yes, it IS a dimvar! + #--------------------- + varid <- nc$dim[[i]]$dimvarid # note: an object of class 'ncid4'. $id will be -1 if there is no dimvar + if( class(varid) != 'ncid4' ) + stop(paste("Internal error #D, returned varid is not a object of class ncid4")) + if( verbose ) + print(paste("vobjtovarid4: returning with DIMvarid deduced from name; varid=", + varid$group_id, varid$id)) + return(varid) # an object of class 'ncid4' + } + } + + #------------------------------------------------------------ + # If we get here, no dimvar with the requested name was found + #------------------------------------------------------------ + print("vobjtovarid4: error #F: I could not find the requsted var (or dimvar) in the file!") + print(paste("var (or dimvar) name:",origvarid)) + print(paste("file name:",nc$filename)) + stop("Variable not found") +} + +.ncvar_id_hier <- function( ncid, varname ) { + + if( mode(ncid) != 'numeric' ) + stop("error, must be passed a numeric first arg: ncid2use") + + if( mode(varname) != 'character' ) + stop("Error, must be passed a character second arg: varname" ) + + rv <- list() + rv$varid <- -1 + rv$groupid <- -1 + rv <- .C("R_nc4_inq_varid_hier", + as.integer(ncid), + as.character(varname), + groupid=as.integer(rv$groupid), + varid=as.integer(rv$varid), + PACKAGE="easyNCDF") + + retval = c( rv$varid, rv$groupid ) + return( retval ) +} + +.default_missval_ncdf4 <- function() +{ + return(1.e30) +} + +.ncvar_get <- function( nc, varid=NA, start=NA, count=NA, verbose=FALSE, signedbyte=TRUE, collapse_degen=TRUE, raw_datavals=FALSE ) { + + if( class(nc) != "ncdf4" ) + stop("first argument (nc) is not of class ncdf4!") + + if( verbose ) print(paste("ncvar_get: entering for read from file", nc$filename)) + + if( (mode(varid) != 'character') && (class(varid) != 'ncvar4') && (class(varid) != 'ncdim4') && (! is.na(varid))) + stop(paste("Error: second argument to ncvar_get must be an object of type ncvar or ncdim", + "(both parts of the ncdf object returned by nc_open()), the character-string name of a variable or dimension", + "or NA to get the default variable from the file. If the file is netcdf version 4", + "format and uses groups, then the fully qualified var name must be given, for", + "example, model1/run5/Temperature")) + + + #---------------------------------------------------- + # If we are running in safemode, must reopen the file + #---------------------------------------------------- + if( nc$safemode ) { + if( verbose ) print(paste("ncvar_get: safemode opening file")) + nc$id = .ncdf4_inner_open( nc ) + } + + idobj = .vobjtovarid4( nc, varid, verbose=verbose, allowdimvar=TRUE ) + + have_start = (length(start)>1) || ((length(start)==1) && (!is.na(start))) + have_count = (length(count)>1) || ((length(count)==1) && (!is.na(count))) + + #----------------------------------------------------------------- + # If we have a start or count, they must not have any NA's in them + #----------------------------------------------------------------- + if( have_start ) { + for( i in 1:length(start)) { + if( is.na(start[i])) + stop(paste("Error, passed a 'start' argument that has NA values:", + paste(start,collapse=' ') )) + } + } + if( have_count ) { + for( i in 1:length(count)) { + if( is.na(count[i])) + stop(paste("Error, passed a 'count' argument that has NA values:", + paste(count,collapse=' ') )) + } + } + + #--------------------------------------------------------------------- + # Special check: if we are trying to get values from a dimvar, but the + # dim does not have a dimvar, then just return 1:length(dim) + #--------------------------------------------------------------------- + if( idobj$isdimvar ) { + if( verbose ) print(paste("ncvar_get: passed object is a dimvar")) + if( idobj$id == -1 ) { # this happens if dim name was passed, but it has no dimvar + #-------------------------------------------------------- + # Here we return default integers for dims with no dimvar + #-------------------------------------------------------- + if( ! have_start ) + start <- 1 + if( ! have_count ) + count <- nc$dim[[idobj$list_index]]$len + if( count == 1 ) + return( start ) + else + return( start:(start+count-1) ) + } + else + { + #----------------------------------------------------------- + # Dimvars do not have list_index set, since dimvars do not + # appear on the global var list. However, dimvars should + # also not have missing values, addOffsets, or scaleFactors, + # so this is easy + #----------------------------------------------------------- + return( .ncvar_get_inner( idobj$group_id, idobj$id, .default_missval_ncdf4(), + start=start, count=count, verbose=verbose, signedbyte=signedbyte )) + } + } + else + { + if( verbose ) print(paste("ncvar_get: passed object is NOT a dimvar")) + } + + #-------------------------------------------- + # Get var's missval, addOffset, and scaleFact + #-------------------------------------------- + if( verbose ) print(paste("ncvar_get: getting add offset and scale fact")) + if( idobj$list_index == -1 ) { + print("internal error: list_index for var is -1!") + print("Here is passed varid:") + print(varid) + } + li = idobj$list_index + if( verbose ) { + print(paste("ncvar_get: netcdf file index of var on list:", li)) + print(paste("ncvar_get: here is var object:")) + print(nc$var[[li]]) + } + if( nc$var[[li]]$hasAddOffset ) + addOffset = nc$var[[li]]$addOffset + else + addOffset = 0; + if( nc$var[[li]]$hasScaleFact ) + scaleFact = nc$var[[li]]$scaleFact + else + scaleFact = 1.0; + + ncid2use = idobj$group_id + varid2use = idobj$id + if( verbose ) print(paste("ncvar_get: ncid2use=", ncid2use, "varid2use=", varid2use, "missval=", nc$var[[li]]$missval )) + + #----------------------------------------------------------- + # If we are in safe mode, must renew our group id and var id + #----------------------------------------------------------- + if( nc$safemode ) { + if(verbose) print(paste('ncvar_get: file is in safe mode, so reopening file', nc$filename)) + nc$id = .ncdf4_inner_open( nc ) + c_varid_gid = .ncvar_id_hier( nc$id, nc$var[[li]]$name ) + varid2use = c_varid_gid[1] + ncid2use = c_varid_gid[2] + if(verbose) print(paste('ncvar_get: safe mode renewed ncid, varid2use:', ncid2use, varid2use )) + } + + rv = .ncvar_get_inner( ncid2use, varid2use, nc$var[[li]]$missval, + addOffset, scaleFact, start=start, count=count, + verbose=verbose, signedbyte=signedbyte, + collapse_degen=collapse_degen, + raw_datavals=raw_datavals ) + + #---------------------------------------------------------------- + # If we are running in safe mode, close the file before returning + #---------------------------------------------------------------- + if( nc$safemode ) { + trv = .C("R_nc4_close", as.integer(nc$id), PACKAGE="easyNCDF") + nc$id = -1 # invalidate this ID since it's not valid any more (duh) + } + + return( rv ) +} diff --git a/cleanup b/cleanup new file mode 100755 index 0000000..435340c --- /dev/null +++ b/cleanup @@ -0,0 +1,4 @@ +#! /bin/sh + +rm -f config.* R/load.R src/Makevars +rm -rf autom4te.cache diff --git a/configure b/configure new file mode 100755 index 0000000..55a4b39 --- /dev/null +++ b/configure @@ -0,0 +1,4095 @@ +#! /bin/sh +# Guess values for system-dependent variables and create Makefiles. +# Generated by GNU Autoconf 2.68. +# +# +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software +# Foundation, Inc. +# +# +# This configure script is free software; the Free Software Foundation +# gives unlimited permission to copy, distribute and modify it. +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## + +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi + + +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. 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But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE + +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +if test "x$CONFIG_SHELL" = x; then + as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST +else + case \`(set -o) 2>/dev/null\` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi +" + as_required="as_fn_return () { (exit \$1); } +as_fn_success () { as_fn_return 0; } +as_fn_failure () { as_fn_return 1; } +as_fn_ret_success () { return 0; } +as_fn_ret_failure () { return 1; } + +exitcode=0 +as_fn_success || { exitcode=1; echo as_fn_success failed.; } +as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } +as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } +as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } +if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : + +else + exitcode=1; echo positional parameters were not saved. +fi +test x\$exitcode = x0 || exit 1" + as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO + as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO + eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && + test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1" + if (eval "$as_required") 2>/dev/null; then : + as_have_required=yes +else + as_have_required=no +fi + if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : + +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_found=false +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + as_found=: + case $as_dir in #( + /*) + for as_base in sh bash ksh sh5; do + # Try only shells that exist, to save several forks. + as_shell=$as_dir/$as_base + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : + CONFIG_SHELL=$as_shell as_have_required=yes + if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : + break 2 +fi +fi + done;; + esac + as_found=false +done +$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : + CONFIG_SHELL=$SHELL as_have_required=yes +fi; } +IFS=$as_save_IFS + + + if test "x$CONFIG_SHELL" != x; then : + # We cannot yet assume a decent shell, so we have to provide a + # neutralization value for shells without unset; and this also + # works around shells that cannot unset nonexistent variables. + # Preserve -v and -x to the replacement shell. + BASH_ENV=/dev/null + ENV=/dev/null + (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV + export CONFIG_SHELL + case $- in # (((( + *v*x* | *x*v* ) as_opts=-vx ;; + *v* ) as_opts=-v ;; + *x* ) as_opts=-x ;; + * ) as_opts= ;; + esac + exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"} +fi + + if test x$as_have_required = xno; then : + $as_echo "$0: This script requires a shell more modern than all" + $as_echo "$0: the shells that I found on your system." + if test x${ZSH_VERSION+set} = xset ; then + $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" + $as_echo "$0: be upgraded to zsh 4.3.4 or later." + else + $as_echo "$0: Please tell bug-autoconf@gnu.org about your system, +$0: including any error possibly output before this +$0: message. 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" >&6; } +if ${ac_cv_objext+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + for ac_file in conftest.o conftest.obj conftest.*; do + test -f "$ac_file" || continue; + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? 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" >&6; } +if ${ac_cv_c_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_compiler_gnu=yes +else + ac_compiler_gnu=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if ${ac_cv_prog_cc_g+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +else + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if ${ac_cv_prog_cc_c89+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg +fi +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac +if test "x$ac_cv_prog_cc_c89" != xno; then : + +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + if test "z$GCC" = zyes; then + NETCDF_IS_GCC=1 + fi + fi + NETCDF_IS_CLANG=0 + if echo "$NETCDF_CC_ARG1" | grep -q "clang"; then + NETCDF_IS_CLANG=1 + fi + + R_IS_GCC=0 + if echo "$R_CC_ARG1" | grep -q "gcc"; then + R_IS_GCC=1 + else + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in $R_CC_ARG1 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in $R_CC_ARG1 +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + + +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "no acceptable C compiler found in \$PATH +See \`config.log' for more details" "$LINENO" 5; } + +# Provide some information about the compiler. +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if ${ac_cv_c_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_compiler_gnu=yes +else + ac_compiler_gnu=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if ${ac_cv_prog_cc_g+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +else + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if ${ac_cv_prog_cc_c89+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg +fi +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac +if test "x$ac_cv_prog_cc_c89" != xno; then : + +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + if test "z$GCC" = zyes; then + R_IS_GCC=1 + fi + fi + R_IS_CLANG=0 + if echo "$R_CC_ARG1" | grep -q "clang"; then + R_IS_CLANG=1 + fi + + #------------------------------------------------------------- + # We don't bother emitting the warning if the two compilers in + # use are clang and gcc -- supposedly they are compatible + #------------------------------------------------------------- + if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_GCC -eq 1; then + emit_warning=0 + fi + if test $NETCDF_IS_GCC -eq 1 -a $R_IS_CLANG -eq 1; then + emit_warning=0 + fi + + #----------------------------------------------------- + # Both same, but different exact names of compilers... + # not sure if this actually guarantees success?? + #----------------------------------------------------- + if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_CLANG -eq 1; then + emit_warning=0 + fi + if test $NETCDF_IS_GCC -eq 1 -a $R_IS_GCC -eq 1; then + emit_warning=0 + fi + + echo "netcdf cc arg1: $NETCDF_CC_ARG1 R cc arg1: $R_CC_ARG1 R_IS_GCC: $R_IS_GCC R_IS_CLANG: $R_IS_CLANG NETCDF_IS_GCC: $NETCDF_IS_GCC NETCDF_IS_CLANG: $NETCDF_IS_CLANG emit_warning: $emit_warning" + + if test $emit_warning -eq 1 -o $TEST_EMIT_WARNING -eq 1; then + echo " " + echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" + echo "Dear ncdf4 user: The software configuration tool thinks that perhaps different compilers are being" + echo "used for R and the netcdf library. However, we all know that software configuration tools are" + echo "not that smart. If ncdf4 compiles fine for you, then please ignore this message. However, if" + echo "installation fails, it might be that you are using different compilers for R and the netcdf library." + echo "If so, then you must create a new version of the netcdf library that was compiled with the same" + echo "compiler that was used to install R (see information above). Then, try installing the ncdf4" + echo "package again using that new netcdf library. If necessary, you can specify the location of" + echo "the new nc-config (the one that uses the same compiler used by R) like this:" + echo " " + echo "R CMD INSTALL --configure-args=\"--with-nc-config=/home/joe/bin/nc-config\"" + echo " " + echo "(obviously, put in the correct path to YOUR nc-config, don't just use my example location!)" + echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" + echo " " + fi + +fi + diff --git a/src/Makevars.in b/src/Makevars.in new file mode 100644 index 0000000..9175e8e --- /dev/null +++ b/src/Makevars.in @@ -0,0 +1,6 @@ +##PKG_CPPFLAGS=-I/path/to/netcdf/header +##PKG_LIBS=-L/path/to/netcdf/lib -lnetcdf + +PKG_LIBS=@NETCDF_LDFLAGS@ +PKG_CPPFLAGS=@NETCDF_CPPFLAGS@ + diff --git a/src/Makevars.win b/src/Makevars.win new file mode 100644 index 0000000..15d0204 --- /dev/null +++ b/src/Makevars.win @@ -0,0 +1 @@ +PKG_LIBS = -lnetcdf4 -L$(LIB_HDF5)/lib${R_ARCH} -lhdf5_hl -lhdf5 -lz diff --git a/src/easyNCDF.c b/src/easyNCDF.c new file mode 100644 index 0000000..b4408b0 --- /dev/null +++ b/src/easyNCDF.c @@ -0,0 +1,733 @@ +/* The functions in this file are copies of some functions in 'ncdf4' package, + * in order for the bugfix in .ncvar_get_inner in easyNCDF to work. When ncdf4 + * addresses this bug, these function will be removed from this package. + * This code belongs to David Pierce. + */ +#include +#include +#include +#include + +#include +#include + +/* These same values are hard-coded into the R source. Don't change them! + * Note that they are not the same as values defined in the netcdf + * library headers, since I don't want my R code to depend on those + */ +#define R_NC_TYPE_SHORT 1 +#define R_NC_TYPE_INT 2 +#define R_NC_TYPE_FLOAT 3 +#define R_NC_TYPE_DOUBLE 4 +#define R_NC_TYPE_TEXT 5 +#define R_NC_TYPE_BYTE 6 + +/* New types in netcdf version 4 */ +#define R_NC_TYPE_UBYTE 7 +#define R_NC_TYPE_USHORT 8 +#define R_NC_TYPE_UINT 9 +#define R_NC_TYPE_INT64 10 +#define R_NC_TYPE_UINT64 11 +#define R_NC_TYPE_STRING 12 + +int R_nc4_nctype_to_Rtypecode( nc_type nct ); +void R_nc4_varsize( int *ncid, int *varid, int *ndims, int *varsize, int *retval ); +void R_nc4_inq_vartype( int *ncid, int *varid, int *precint, int *retval ); +void R_nc4_inq_varndims( int *ncid, int *varid, int *ndims, int *retval ); +void R_nc4_open( char **filename, int *cmode, int *ncid, int *retval ); +void R_nc4_get_vara_text( int *ncid, int *varid, int *start, int *count, char **tempstore, char **data, int *retval ); +void R_nc4_close ( int *ncid ); +SEXP Rsx_nc4_get_vara_double( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count, SEXP sx_fixmiss, SEXP sx_imvstate, SEXP sx_missval ); +SEXP Rsx_nc4_get_vara_int ( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count, SEXP sx_byte_style ); +SEXP R_nc4_blankstring(SEXP size); +SEXP R_nc4_get_vara_string( SEXP sx_nc, SEXP sx_varid, SEXP sx_start, SEXP sx_count ); +void R_nc4_inq_varid_hier( int *ncid, char **varname, int *returned_grpid, int *returned_varid ); + +// Non-registered +int R_nc4_util_nslashes( char *s, int *idx_first_slash ); +void R_nc4_inq_varid_hier_inner( int *ncid, char *varname, int *returned_grpid, int *returned_varid ); + +/* For C calls that don't use SEXP type args */ +static const +R_CMethodDef cMethods[] = { + {"R_nc4_inq_varid_hier", (DL_FUNC) &R_nc4_inq_varid_hier, 4}, + {"R_nc4_nctype_to_Rtypecode", (DL_FUNC) &R_nc4_nctype_to_Rtypecode, 1}, + {"R_nc4_varsize", (DL_FUNC) &R_nc4_varsize, 5}, + {"R_nc4_inq_vartype", (DL_FUNC) &R_nc4_inq_vartype, 4}, + {"R_nc4_inq_varndims", (DL_FUNC) &R_nc4_inq_varndims, 4}, + {"R_nc4_open", (DL_FUNC) &R_nc4_open, 4}, + {"R_nc4_get_vara_text", (DL_FUNC) &R_nc4_get_vara_text, 7}, + {"R_nc4_close", (DL_FUNC) &R_nc4_close, 1}, + NULL +}; + +/* For C calls that use SEXP type args */ +static const +R_CallMethodDef callMethods[] = { + {"Rsx_nc4_get_vara_double", (DL_FUNC) &Rsx_nc4_get_vara_double, 7}, + {"Rsx_nc4_get_vara_int", (DL_FUNC) &Rsx_nc4_get_vara_int, 5}, + {"R_nc4_blankstring", (DL_FUNC) &R_nc4_blankstring, 1}, + {"R_nc4_get_vara_string", (DL_FUNC) &R_nc4_get_vara_string, 4}, + NULL +}; + +/********************************************************************* + * Register our extnal routines for R +*/ +void R_init_ncdf4( DllInfo *info ) +{ + R_registerRoutines( info, cMethods, callMethods, NULL, NULL ); + R_useDynamicSymbols( info, FALSE ); +} + +/********************************************************************* + * Converts from type "nc_type" to an integer as defined in the beginning + * of this file. We do NOT use the raw nc_type integers because then the + * R code would have a dependency on the arbitrary values in the netcdf + * header files! + */ +int R_nc4_nctype_to_Rtypecode( nc_type nct ) +{ + if( nct == NC_CHAR ) + return(R_NC_TYPE_TEXT); + else if( nct == NC_SHORT ) + return(R_NC_TYPE_SHORT); + else if( nct == NC_INT ) + return(R_NC_TYPE_INT); + else if( nct == NC_FLOAT ) + return(R_NC_TYPE_FLOAT); + else if( nct == NC_DOUBLE ) + return(R_NC_TYPE_DOUBLE); + else if( nct == NC_BYTE ) + return(R_NC_TYPE_BYTE); + + else if( nct == NC_UBYTE ) + return(R_NC_TYPE_UBYTE); + else if( nct == NC_USHORT ) + return(R_NC_TYPE_USHORT); + else if( nct == NC_UINT ) + return(R_NC_TYPE_UINT); + else if( nct == NC_INT64 ) + return(R_NC_TYPE_INT64); + else if( nct == NC_UINT64 ) + return(R_NC_TYPE_UINT64); + else if( nct == NC_STRING ) + return(R_NC_TYPE_STRING); + else + return(-1); +} + +/*********************************************************************/ +/* Returns a vector of dim sizes for the variable. + * 'retval' is 0 for no error, or -1 for an error. + */ +void R_nc4_varsize( int *ncid, int *varid, int *ndims, int *varsize, int *retval ) +{ + int i, err, dimid[NC_MAX_DIMS]; + size_t dimlen; + + *retval = 0; + + /* Get ndims */ + err = nc_inq_varndims( *ncid, *varid, ndims ); + if( err != NC_NOERR ) { + Rprintf( "Error in R_nc4_varsize on nc_inq_varndims call: %s\n", + nc_strerror(err) ); + *retval = -1; + return; + } + + /* Get dimids */ + err = nc_inq_vardimid( *ncid, *varid, dimid ); + if( err != NC_NOERR ) { + Rprintf( "Error in R_nc4_varsize on nc_inq_vardimid call: %s\n", + nc_strerror(err) ); + *retval = -1; + return; + } + + /* Get size of each dim */ + for( i=0; i<(*ndims); i++ ) { + err = nc_inq_dimlen( *ncid, dimid[i], &dimlen ); + if( err != NC_NOERR ) { + Rprintf( "Error in R_nc4_varsize on nc_inq_dimlen call: %s\n", + nc_strerror(err) ); + *retval = -1; + return; + } + varsize[i] = (int)dimlen; + } +} + +/*********************************************************************/ +void R_nc4_inq_vartype( int *ncid, int *varid, int *precint, int *retval ) +{ + nc_type nct; + + *retval = nc_inq_vartype( *ncid, *varid, &nct ); + + if( *retval != NC_NOERR ) + Rprintf( "Error in R_nc4_inq_var: %s\n", + nc_strerror(*retval) ); + + *precint = R_nc4_nctype_to_Rtypecode(nct); +} + +/*********************************************************************/ +void R_nc4_inq_varndims( int *ncid, int *varid, int *ndims, int *retval ) +{ + *retval = nc_inq_varndims(*ncid, *varid, ndims ); + if( *retval != NC_NOERR ) + Rprintf( "Error in R_nc4_inq_varndims: %s\n", + nc_strerror(*retval) ); +} + +/*********************************************************************/ +/* Inputs: + * sx_fixmiss : is 1 if we want to fix the missing values in this + * routine, and 0 otherwise + * sx_imvstate : 0=var has no missing value; 1=var has a NA for + * the missing value; 2=var has a valid, non-NA missing value + * + * Returns a list with elements: + * $error : 0 for success, -1 for error + * $data : array of integer values read in from the netcdf file + */ +SEXP Rsx_nc4_get_vara_double( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count, + SEXP sx_fixmiss, SEXP sx_imvstate, SEXP sx_missval ) +{ + SEXP sx_retval, sx_retnames, sx_reterr, sx_retdata; + int ncid, varid, i, err, ndims, fixmiss, imvstate, scalar_var; + double *p_data, missval, mvtol; + size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS], tot_size; + char vn[2048]; + + /* Make space for our returned list, which will have + * two elements, named $error and $data + */ + PROTECT( sx_retval = allocVector( VECSXP, 2 )); /* 2 elements in returned list */ + + /* Set names for the returned list */ + PROTECT( sx_retnames = allocVector( STRSXP, 2 )); + SET_STRING_ELT( sx_retnames, 0, mkChar("error") ); + SET_STRING_ELT( sx_retnames, 1, mkChar("data" ) ); + setAttrib( sx_retval, R_NamesSymbol, sx_retnames ); + UNPROTECT(1); /* done with sx_retnames */ + + /* Set provisional 'no error' retval */ + PROTECT(sx_reterr = allocVector( INTSXP, 1 )); + INTEGER(sx_reterr)[0] = 0; + + ncid = INTEGER(sx_ncid )[0]; + varid = INTEGER(sx_varid )[0]; + fixmiss = INTEGER(sx_fixmiss )[0]; + imvstate = INTEGER(sx_imvstate)[0]; + missval = REAL (sx_missval )[0]; + + /* Get number of dimensions in this variable */ + err = nc_inq_varndims( ncid, varid, &ndims ); + if( err != NC_NOERR ) { + Rprintf( "Error in R_nc4_get_vara_double while getting ndims: %s\n", + nc_strerror(err) ); + INTEGER(sx_reterr)[0] = -1; + SET_VECTOR_ELT( sx_retval, 0, sx_reterr ); + UNPROTECT(2); + return( sx_retval ); + } + + /* Sanity check -- number of start and count elements must + match number of dims in the var + */ + scalar_var = ((ndims==0) && (GET_LENGTH(sx_start)==1) && (INTEGER(sx_start)[0]==0) && (INTEGER(sx_count)[0]==1)); + if( (!scalar_var) && (ndims != GET_LENGTH(sx_start))) { + Rprintf( "Error in R_nc4_get_vara_double: I think var has %d dimensions, but passed start array is length %d. They must be the same!\n", + ndims, GET_LENGTH(sx_start) ); + INTEGER(sx_reterr)[0] = -1; + SET_VECTOR_ELT( sx_retval, 0, sx_reterr ); + UNPROTECT(2); + return( sx_retval ); + } + + if( (!scalar_var) && (ndims != GET_LENGTH(sx_count))) { + Rprintf( "Error in R_nc4_get_vara_double: I think var has %d dimensions, but passed count array is length %d. They must be the same!\n", + ndims, GET_LENGTH(sx_count) ); + INTEGER(sx_reterr)[0] = -1; + SET_VECTOR_ELT( sx_retval, 0, sx_reterr ); + UNPROTECT(2); + return( sx_retval ); + } + + /* Get total number of elements we will be reading so we can + * allocate R space + */ + tot_size = 1L; + for( i=0; i= 0"); + + str = R_alloc(len + 1, sizeof(char)); + for (i = 0; i < len; ++i) + str[i] = ' '; + str[len] = '\0'; + + blank = PROTECT(NEW_CHARACTER(1)); + string = PROTECT(mkChar(str)); + SET_STRING_ELT(blank, 0, string); + UNPROTECT(2); + + return(blank); +} + +/********************************************************************************* + * Read vlen strings given the numeric varid, start, and count to use + */ +SEXP R_nc4_get_vara_string( SEXP sx_nc, SEXP sx_varid, SEXP sx_start, SEXP sx_count ) +{ + SEXP sx_retval, sx_retnames, sx_retstrings, sx_reterror; + int i, ierr, nchar, varid, ncid, ndims, count_int[MAX_NC_DIMS], start_int[MAX_NC_DIMS], len_count, len_start; + size_t count[MAX_NC_DIMS], start[MAX_NC_DIMS], tot_count, isz; + char **ss; + + /* Convert passed parameters (which are in R format) into C format */ + ncid = INTEGER(sx_nc )[0]; + varid = INTEGER(sx_varid)[0]; + + len_start = length(sx_start); + for( i=0; i%s<\n", varname ); */ + + /* Passed var name must not start with a slash */ + if( varname[0] == '/' ) { + Rprintf( "Error in R_nc4_varid_hier: passed varname must not start with a slash!\n" ); + *returned_varid = -1; + *returned_grpid = -1; + return; + } + + /* If there are no forward slashes in the name, then it is a simple var name */ + nslashes = R_nc4_util_nslashes( varname, &idx_first_slash ); +/* Rprintf("R_nc4_inq_varid_hier_inner: varname >%s< has nslashes=%d and idx first slash=%d\n", varname, nslashes, idx_first_slash ); */ + if( nslashes == 0 ) { + *returned_grpid = *ncid; + ierr = nc_inq_varid(*ncid, varname, returned_varid ); + if( ierr != NC_NOERR ) { + *returned_varid = -1; + *returned_grpid = -1; + } +/* Rprintf("R_nc4_inq_varid_hier_inner: Found id for var >%s< varid:%d gid:%d\n", varname, *returned_varid, *returned_grpid ); */ + return; + } + + /* If we get here then the varname must have at least one slash, which indicates + * a group name under the current group name. Get the ID of that group + */ + strncpy( gname, varname, idx_first_slash ); + gname[ idx_first_slash ] = '\0'; + ierr = nc_inq_grp_ncid( *ncid, gname, &gid ); + if( ierr != NC_NOERR ) { + Rprintf( "Error in R_nc4_varid_hier: extracted groupname not found: >%s< (coding error?)\n", gname ); + *returned_varid = -1; + *returned_grpid = -1; + return; + } + + /* Call ourselves recursively with the subgroup id and the varname stripped + * of its leading group name + */ +/* Rprintf("R_nc4_inq_varid_hier_inner: calling myself recursively with varname=>%s<\n", varname+idx_first_slash+1 ); */ + R_nc4_inq_varid_hier_inner( &gid, varname+idx_first_slash+1, returned_grpid, returned_varid ); +} + +/****************************************************************************************/ +/* This version of inq_varid works with hierarchial var names such as "model1/TS" and + * returns both the group ID and the var ID in that group, given the root group id + * (netcdf file ID). + * + * If the passed var is not found in the file, then -1 is returned. + * + * The passed slash-ful varname must not start or end with a slash. + */ +void R_nc4_inq_varid_hier( int *ncid, char **varname, int *returned_grpid, int *returned_varid ) +{ +/* Rprintf("R_nc4_inq_varid_hier: entering for var >%s<\n", varname[0] ); */ + R_nc4_inq_varid_hier_inner( ncid, varname[0], returned_grpid, returned_varid ); +} -- GitLab