Fix various check issues that appear in the newest version

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: hdf5r
 Type: Package
 Title: Interface to the 'HDF5' Binary Data Format
-Version: 1.3.8
+Version: 1.3.9
 Authors@R: c(
     person("Holger", "Hoefling", email = "[email protected]", role = c("aut", "cre")),
     person("Mario", "Annau", email = "[email protected]", role = "aut"),

Makefile

@@ -1,6 +1,7 @@
 .ONESHELL:
+SHELL:=/bin/bash
 
-R_REVISION?=83640
+R_REVISION?=85786
 HDF5_VERSION?=System
 DOCKER_CRAN_CHECK_ARG=''
 # DOCKER_CRAN_CHECK_ARG='--as-cran'
@@ -14,7 +15,7 @@ PKG_NAME := $(shell grep -i ^package DESCRIPTION | cut -d : -d \  -f 2)
 #DATA_FILES := $(wildcard data/*.rda)
 R_FILES := $(wildcard R/*.R)
 TEST_FILES := $(wildcard tests/*.R) $(wildcard tests/testthat/*.R)
-ALL_SRC_FILES := $(wildcard src/*.cpp) $(wildcard src/*.h) src/Makevars.in
+ALL_SRC_FILES := $(wildcard src/*.c) $(wildcard src/*.h) src/Makevars.in
 RMD_FILES := README.Rmd
 MD_FILES := $(RMD_FILES:.Rmd=.md)
 SRC_FILES := $(filter-out src/RcppExports.cpp, $(ALL_SRC_FILES))
@@ -71,6 +72,7 @@ check: $(BUILD_OUTPUT)
 
 check-docker: $(BUILD_OUTPUT)
 	if [[ "${HDF5_VERSION}" = "System" ]]; then
+		echo HDF is System
 		$(MAKE) -C docker build-system R_REVISION=${R_REVISION} HDF5_VERSION=${HDF5_VERSION}
 	else
 		$(MAKE) -C docker build-custom R_REVISION=${R_REVISION} HDF5_VERSION=${HDF5_VERSION}

R/convert.R

@@ -372,22 +372,20 @@ guess_chunks <- function(space_maxdims, dtype_size, chunk_size=getOption("hdf5r.
     return(chunk_dim)
 }
 
-##' Set the correct dimension attribute for an object
+##' Get the correct dimensions for a space and datatype
 ##'
-##' This function uses the space and the selection in it to set the correct dimension
+##' This function uses the space and the selection in it to get the correct dimension
 ##' for the resulting object (but without dropping dimensions). Furthermore, if the
 ##' datatype is an array, those dimensions are correctly determined as well.
 ##'
 ##' Internal use only; currently unused
-##' @title Set the correct dimension attribute for an object
-##' @param x an object that was read from an HDF5 dataset or attribute
+##' @title Extract the dimension of a space and datatype
 ##' @param space The space with the selection that was used to read the dataset
 ##' @param dtype The datatype of the dataset
 ##' @return \code{x}, but with a new dimension attribute
 ##' @author Holger Hoefling
 ##' @keywords internal
 extract_dim <- function(space, dtype) {
-    ## apply the right dimension attribute to x that is implied by the space and the data-type
     dtype_dim <- NULL
     if(inherits(dtype, "H5T")) {
         if(dtype$get_class() == h5const$H5T_ARRAY) {

R/high_level_UI.R

@@ -348,7 +348,7 @@ are_args_scalar <- function(args) {
 ##'
 ##' Checks for the functions \code{:}, \code{seq} and \code{seq_len}
 ##' @title Check argument for known functions that encode a hyperslab
-##' @param cur_arg The argument to check
+##' @param x The argument to check
 ##' @param envir The environment in which to evaluate the argument
 ##' @return A vector of length 4 describing start, count, stride and block if appropriate
 ##' @author Holger Hoefling

inst/CWrappers_1.10.0/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.10.0/identify_prototypes.R

@@ -318,7 +318,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.10.2/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.10.2/identify_prototypes.R

@@ -318,7 +318,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.10.3/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.10.3/identify_prototypes.R

@@ -318,7 +318,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.12.0/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.12.0/identify_prototypes.R

@@ -321,7 +321,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.8.12/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.8.12/identify_prototypes.R

@@ -318,7 +318,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.8.14/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.8.14/identify_prototypes.R

@@ -319,7 +319,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

inst/CWrappers_1.8.16/datatype_export_c.brew

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

inst/CWrappers_1.8.16/identify_prototypes.R

@@ -318,7 +318,7 @@ struct_all_elements_rtype$all_rtype[struct_all_elements_rtype$category_name=="H5
 struct_all_elements_rtype <- subset(struct_all_elements_rtype, all_rtype)
 
 
-all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") ||
+all_types_with_complete_rtype <- rbind.fill(subset(struct_enum_types, !category %in% c("struct", "union") |
                                                category_name %in% struct_all_elements_rtype$category_name), all_other)
 all_types_with_complete_rtype <- subset(all_types_with_complete_rtype, has_rtype)
 

src/1_10_0/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_10_2/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_10_3/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_12_0/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_8_12/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_8_14/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/1_8_16/datatype_export.c

@@ -64,7 +64,7 @@ hid_t get_h5_equiv(int size, bool sign) {
 SEXP print_dtypes_array(void) {
   Rprintf("New -------------------------------------\n");
   for(int i=0; i < DT_LAST_ITEM; ++i) {
-    Rprintf("%d: %I64d\n", i, h5_datatype[i]);
+    Rprintf("%d: %ld\n", i, h5_datatype[i]);
   }
   return(R_NilValue);
 }

src/Wrapper_manual_H5T.c

@@ -73,7 +73,7 @@ SEXP h5create_enum_type(SEXP _labels, SEXP _values, SEXP _dtype_id) {
     H5Tconvert(H5T_NATIVE_LLONG, dtype_id, 1, &buf, NULL, H5P_DEFAULT);
     status = H5Tenum_insert(datatype, CHAR(STRING_ELT(_labels, i)), &buf);
     if(status < 0) {
-      error("Could not insert value into enum %s value %d with status %d\n", CHAR(STRING_ELT(_labels, i)), buf, status);
+      error("Could not insert value into enum %s value %lld with status %d\n", CHAR(STRING_ELT(_labels, i)), buf, status);
     }
   }
 

src/convert.c

@@ -258,7 +258,7 @@ SEXP RToH5_INTEGER(SEXP _Robj, hid_t dtype_id, R_xlen_t nelem) {
   SEXP Rval;
 
   if(nelem != XLENGTH(_Robj)) {
-    error("Length of integer vector not as expected: Actual: %d; Expected %d\n", XLENGTH(_Robj), nelem);
+    error("Length of integer vector not as expected: Actual: %ld; Expected %ld\n", XLENGTH(_Robj), nelem);
   }
 
   switch(TYPEOF(_Robj)) {