Source: libminc Version: 2.3.00-3 Severity: important -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256
Hi, Please find attached a patch to support building against HDF5-1.10 currently in experimental. This patch is a backport of two upstream commits related to hdf5-1.10 support. Please see upstream ticket #74 [1]. [1] https://github.com/BIC-MNI/libminc/issues/74 I intend to request a transition slot this week, and will NMU if need be. Thanks, _g. - -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.6.0-1-amd64 (SMP w/2 CPU cores) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -----BEGIN PGP SIGNATURE----- iQEcBAEBCAAGBQJYDnQdAAoJEO/obGx//s+DMucIAKfPWkyHBDzPJIaB4OCqp6dk kwZPq8YbvikQL+y71IXLDNncxytiqQpakbLHhcokK/+DqZu6c5j1tNOnQTRvgaXc oCfLd4Fh5/bYtAGs1TtnCw0FEje3qUtA4in4TEy9lKcuXwVHYrrFOxqiv1N4Xznj GbpvIEjM1nR4IIP2s4zs0ZM0Q437bEV6rZejWnKypB9AlHAQafx2Cf/zG82oYlHX AlqnjUJW3Uoc0IBe6RvOFvt8LHG1vm8HSy+zQBeLGGCoC8b5qc7xiCQVu01G5+sR eocifRf60srli2i4sB0uUsDE1EpE6D+jBRQY/Kw6QNSqbO2g7x5dNvT8BC2zgoA= =JOhL -----END PGP SIGNATURE-----
diff -Nru libminc-2.3.00/debian/changelog libminc-2.3.00/debian/changelog --- libminc-2.3.00/debian/changelog 2016-09-02 09:40:37.000000000 +0200 +++ libminc-2.3.00/debian/changelog 2016-10-20 19:31:12.000000000 +0200 @@ -1,3 +1,10 @@ +libminc (2.3.00-3.1) unstable; urgency=medium + + * Non-maintainer upload + * New patch to support HDF5 1.10 + + -- Gilles Filippini <p...@debian.org> Thu, 20 Oct 2016 19:31:10 +0200 + libminc (2.3.00-3) unstable; urgency=medium * Wrote watch file diff -Nru libminc-2.3.00/debian/patches/hdf5-1.10-support.patch libminc-2.3.00/debian/patches/hdf5-1.10-support.patch --- libminc-2.3.00/debian/patches/hdf5-1.10-support.patch 1970-01-01 01:00:00.000000000 +0100 +++ libminc-2.3.00/debian/patches/hdf5-1.10-support.patch 2016-10-20 20:37:42.000000000 +0200 @@ -0,0 +1,451 @@ +Description: don't assume hid_t === int since this is no longer true + in HDF5 1.10. + This is a backport of upstream commits d99dd01 and 92ba4fa related + to issue #74 [1]. + . + [1] https://github.com/BIC-MNI/libminc/issues/74 +Index: libminc-2.3.00/libsrc/hdf_convenience.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.c ++++ libminc-2.3.00/libsrc/hdf_convenience.c +@@ -45,7 +45,8 @@ struct m2_dim { + + static struct m2_file { + struct m2_file *link; +- hid_t fd; ++ int fd; /* our fake file id */ ++ hid_t file_id; /* actual hdf5 file id */ + int wr_ok; /* non-zero if write OK */ + int resolution; /* Resolution setting. */ + int nvars; +@@ -74,18 +75,20 @@ hdf_id_check(int fd) + } + + static struct m2_file * +-hdf_id_add(int fd) ++hdf_id_add(hid_t file_id) + { + struct m2_file *new; ++ static unsigned short _id = 0; /* at most 2^16 id's */ + + new = (struct m2_file *) malloc(sizeof (struct m2_file)); + if (new != NULL) { +- new->fd = fd; ++ new->fd = HDF5_ID_MIN + _id++; ++ new->file_id = file_id; + new->resolution = 0; + new->nvars = 0; + new->ndims = 0; + new->link =_m2_list; +- new->grp_id = H5Gopen1(fd, MI2_GRPNAME); ++ new->grp_id = H5Gopen1(file_id, MI2_GRPNAME); + new->comp_type = MI2_COMP_UNKNOWN; + new->comp_param = 0; + new->chunk_type = MI2_CHUNK_UNKNOWN; +@@ -99,7 +102,7 @@ hdf_id_add(int fd) + return (new); + } + +-static int ++static int + hdf_id_del(int fd) + { + struct m2_file *curr, *prev; +@@ -142,6 +145,7 @@ hdf_id_del(int fd) + } + + H5Gclose(curr->grp_id); ++ H5Fclose(curr->file_id); + free(curr); + return (MI_NOERROR); + } +@@ -187,7 +191,7 @@ hdf_var_add(struct m2_file *file, const + strncpy(new->name, name, NC_MAX_NAME - 1); + strncpy(new->path, path, NC_MAX_NAME - 1); + new->is_cmpd = 0; +- new->dset_id = H5Dopen1(file->fd, path); ++ new->dset_id = H5Dopen1(file->file_id, path); + new->ftyp_id = H5Dget_type(new->dset_id); + new->mtyp_id = H5Tget_native_type(new->ftyp_id, H5T_DIR_ASCEND); + new->fspc_id = H5Dget_space(new->dset_id); +@@ -490,7 +494,7 @@ hdf_attinq(int fd, int varid, const char + return (MI_ERROR); + } + +- if (varid == NC_GLOBAL) { ++ if (varid == NC_GLOBAL || varid == MI_ROOTVARIABLE_ID) { + var = NULL; + loc_id = file->grp_id; + } +@@ -591,7 +595,7 @@ hdf_attinq(int fd, int varid, const char + } + + static int +-hdf_put_dimorder(struct m2_file *file, int dst_id, int ndims, ++hdf_put_dimorder(struct m2_file *file, hid_t dst_id, int ndims, + const int *dims_ptr) + { + int i; +@@ -626,6 +630,9 @@ hdf_put_dimorder(struct m2_file *file, i + if (att_id >= 0) { + H5Awrite(att_id, typ_id, str_buf); + } ++ else { ++ fprintf(stderr, "Failed to create dimorder %lx\n", dst_id); ++ } + + H5Aclose(att_id); + H5Sclose(spc_id); +@@ -634,7 +641,7 @@ hdf_put_dimorder(struct m2_file *file, i + } + + static int +-hdf_get_dimorder(struct m2_file *file, int dst_id, int ndims, int *dims_ptr) ++hdf_get_dimorder(struct m2_file *file, hid_t dst_id, int ndims, int *dims_ptr) + { + char *str_ptr; + char *tmp_ptr; +@@ -974,7 +981,7 @@ hdf_attget(int fd, int varid, const char + return (MI_ERROR); + } + +- if (varid == NC_GLOBAL) { ++ if (varid == NC_GLOBAL || varid == MI_ROOTVARIABLE_ID) { + var = NULL; + loc_id = file->grp_id; + } +@@ -1120,11 +1127,11 @@ hdf_attput(int fd, int varid, const char + H5Pclose(new_plst_id); + H5Sclose(var->fspc_id); + +- if (H5Gunlink(fd, var->path) < 0) { ++ if (H5Gunlink(file->file_id, var->path) < 0) { + milog_message(MI_MSG_SNH); + } + +- if (H5Gmove2(file->grp_id, temp, fd, var->path) < 0) { ++ if (H5Gmove2(file->grp_id, temp, file->file_id, var->path) < 0) { + milog_message(MI_MSG_SNH); + } + +@@ -1196,7 +1203,7 @@ hdf_attput(int fd, int varid, const char + att_id = H5Acreate2(loc_id, attnm, ftyp_id, spc_id, H5P_DEFAULT, H5P_DEFAULT); + + if (att_id < 0) +- goto cleanup; ++ goto cleanup; + + /* Save the value. + */ +@@ -1261,10 +1268,10 @@ int + hdf_vardef(int fd, const char *varnm, nc_type vartype, int ndims, + const int *dimids) + { +- int dst_id = -1; +- int typ_id = -1; +- int spc_id = -1; +- int prp_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t spc_id = -1; ++ hid_t prp_id = -1; + int status = MI_ERROR; + int i; + long length; +@@ -1392,7 +1399,7 @@ hdf_vardef(int fd, const char *varnm, nc + } + + H5E_BEGIN_TRY { +- dst_id = H5Dcreate2(fd, varpath, typ_id, spc_id, H5P_DEFAULT, prp_id, H5P_DEFAULT); ++ dst_id = H5Dcreate2(file->file_id, varpath, typ_id, spc_id, H5P_DEFAULT, prp_id, H5P_DEFAULT); + } H5E_END_TRY; + + if (dst_id < 0) { +@@ -1465,10 +1472,10 @@ hdf_varget(int fd, int varid, const long + void *val_ptr) + { + int status = MI_ERROR; +- int dst_id = -1; +- int typ_id = -1; +- int fspc_id = -1; +- int mspc_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t fspc_id = -1; ++ hid_t mspc_id = -1; + int i; + int ndims; + hsize_t fstart[MAX_VAR_DIMS]; +@@ -1560,8 +1567,8 @@ hdf_varget(int fd, int varid, const long + } + + int +-hdf_varputg(int fd, int varid, const long *start, +- const long *edges, const long *stride, ++hdf_varputg(int fd, int varid, const long *start, ++ const long *edges, const long *stride, + const long *map, const void *value) + { + int status = MI_ERROR; /* Assume guilty */ +@@ -1577,10 +1584,10 @@ hdf_varputg(int fd, int varid, const lon + + struct m2_var *varp; + struct m2_file *file; +- int dst_id = -1; +- int typ_id = -1; +- int fspc_id = -1; +- int mspc_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t fspc_id = -1; ++ hid_t mspc_id = -1; + + if ((file = hdf_id_check(fd)) == NULL) { + return (MI_ERROR); +@@ -1747,8 +1754,8 @@ hdf_varputg(int fd, int varid, const lon + } + + int +-hdf_vargetg(int fd, int varid, const long *start, +- const long *edges, const long *stride, ++hdf_vargetg(int fd, int varid, const long *start, ++ const long *edges, const long *stride, + const long *map, void *value) + { + int status = MI_NOERROR; +@@ -1910,10 +1917,10 @@ hdf_varput(int fd, int varid, const long + const void *val_ptr) + { + int status = MI_ERROR; +- int dst_id; +- int typ_id; +- int fspc_id; +- int mspc_id = -1; ++ hid_t dst_id; ++ hid_t typ_id; ++ hid_t fspc_id; ++ hid_t mspc_id = -1; + int i; + int ndims; + hsize_t fstart[MAX_VAR_DIMS]; +@@ -2085,6 +2092,7 @@ herr_t hdf_copy_attr(hid_t in_id, const + * don't overwrite the existing value. + */ + status = MI_NOERROR; ++ fprintf(stderr, "Failed to create attribute '%s'\n", attr_name); + goto cleanup; + } + +@@ -2195,7 +2203,7 @@ hdf_open_dsets(struct m2_file *file, hid + int + hdf_open(const char *path, int mode) + { +- hid_t fd; ++ hid_t file_id; + hid_t grp_id; + hid_t dset_id; + struct m2_file *file; +@@ -2210,28 +2218,28 @@ hdf_open(const char *path, int mode) + + prp_id = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mmap(prp_id, 8192, 1); +- fd = H5Fopen(path, mode & 0x7FFF, prp_id); ++ file_id = H5Fopen(path, mode & 0x7FFF, prp_id); + H5Pclose(prp_id); + } + else { +- fd = H5Fopen(path, mode, H5P_DEFAULT); ++ file_id = H5Fopen(path, mode, H5P_DEFAULT); + } + #else +- fd = H5Fopen(path, mode, H5P_DEFAULT); ++ file_id = H5Fopen(path, mode, H5P_DEFAULT); + #endif + } H5E_END_TRY; + +- if (fd < 0) { ++ if (file_id < 0) { + return (MI_ERROR); + } + +- file = hdf_id_add(fd); /* Add it to the list */ ++ file = hdf_id_add(file_id); /* Add it to the list */ + file->wr_ok = (mode & H5F_ACC_RDWR) != 0; + + /* Open the image variables. + */ + H5E_BEGIN_TRY { +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image"); + if (dset_id >= 0) { + hid_t type_id; + int is_compound = 0; +@@ -2262,7 +2270,7 @@ hdf_open(const char *path, int mode) + H5Dclose(dset_id); + } + +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image-min"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image-min"); + if (dset_id >= 0) { + hdf_get_diminfo(dset_id, &ndims, dims); + hdf_var_add(file, MIimagemin, "/minc-2.0/image/0/image-min", +@@ -2270,7 +2278,7 @@ hdf_open(const char *path, int mode) + H5Dclose(dset_id); + } + +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image-max"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image-max"); + if (dset_id >= 0) { + hdf_get_diminfo(dset_id, &ndims, dims); + hdf_var_add(file, MIimagemax, "/minc-2.0/image/0/image-max", +@@ -2281,16 +2289,16 @@ hdf_open(const char *path, int mode) + + /* Open all of the datasets in the "dimensions" category. + */ +- grp_id = H5Gopen2(fd, "/minc-2.0/dimensions", H5P_DEFAULT); ++ grp_id = H5Gopen2(file_id, "/minc-2.0/dimensions", H5P_DEFAULT); + hdf_open_dsets(file, grp_id, "/minc-2.0/dimensions/", 1); + H5Gclose(grp_id); + + /* Open all of the datasets in the "info" category. + */ +- grp_id = H5Gopen2(fd, "/minc-2.0/info", H5P_DEFAULT); ++ grp_id = H5Gopen2(file_id, "/minc-2.0/info", H5P_DEFAULT); + hdf_open_dsets(file, grp_id, "/minc-2.0/info/", 0); + H5Gclose(grp_id); +- return (fd); ++ return (file->fd); + } + + /** Create an HDF5 file. */ +@@ -2298,7 +2306,7 @@ int + hdf_create(const char *path, int cmode, struct mi2opts *opts_ptr) + { + hid_t grp_id; +- hid_t fd; ++ hid_t file_id; + hid_t tmp_id; + struct m2_file *file; + hid_t hdf_gpid; +@@ -2319,10 +2327,10 @@ hdf_create(const char *path, int cmode, + H5Pset_libver_bounds (fpid, H5F_LIBVER_18, H5F_LIBVER_18); + + H5E_BEGIN_TRY { +- fd = H5Fcreate(path, cmode, H5P_DEFAULT, fpid); ++ file_id = H5Fcreate(path, cmode, H5P_DEFAULT, fpid); + } H5E_END_TRY; +- if (fd < 0) { +- fprintf(stderr, "Error creating HDF file '%s' with mode '%x', result %d\n", path, cmode, fd); ++ if (file_id < 0) { ++ fprintf(stderr, "Error creating HDF file '%s' with mode '%x', result %d\n", path, cmode, (int)file_id); + H5Eprint1(stderr); + return (MI_ERROR); + } +@@ -2332,7 +2340,7 @@ hdf_create(const char *path, int cmode, + /* Create the default groups. + * Should we use a non-zero value for size_hint (parameter 3)??? + */ +- if ((grp_id = H5Gcreate2(fd, MI2_GRPNAME, H5P_DEFAULT, hdf_gpid, H5P_DEFAULT)) < 0) { ++ if ((grp_id = H5Gcreate2(file_id, MI2_GRPNAME, H5P_DEFAULT, hdf_gpid, H5P_DEFAULT)) < 0) { + fprintf(stderr, "Error creating groups on line %d\n", __LINE__); + H5Eprint1(stderr); + return (MI_ERROR); +@@ -2369,7 +2377,7 @@ hdf_create(const char *path, int cmode, + H5Gclose(tmp_id); + H5Gclose(grp_id); + +- file = hdf_id_add(fd); /* Add it to the list */ ++ file = hdf_id_add(file_id); /* Add it to the list */ + if (file == NULL) { + fprintf(stderr, "Error adding ID to list.\n"); + H5Eprint1(stderr); +@@ -2384,7 +2392,7 @@ hdf_create(const char *path, int cmode, + file->chunk_type = opts_ptr->chunk_type; + file->chunk_param = opts_ptr->chunk_param; + } +- return ((int) fd); ++ return (file->fd); + } + + int +@@ -2392,7 +2400,6 @@ hdf_close(int fd) + { + hdf_dim_commit(fd); /* Make sure all dimensions were saved. */ + hdf_id_del(fd); /* Delete it from the list. */ +- H5Fclose(fd); + return (MI_NOERROR); + } + +@@ -2412,4 +2419,22 @@ hdf_access(const char *path) + return (status > 0); /* Return non-zero if success */ + } + ++/* ++ * Flushes the hdf file to disk ++ */ ++int ++hdf_flush(int fd) ++{ ++ struct m2_file *file; ++ if ((file = hdf_id_check(fd))!=NULL ) { ++ /* Commit the (entire) file to disk. */ ++ if (H5Fflush(file->file_id, H5F_SCOPE_GLOBAL) < 0) { ++ return MI_ERROR; ++ } ++ return MI_NOERROR; ++ } ++ return MI_ERROR; ++} ++ ++ + #endif /* MINC2 defined */ +Index: libminc-2.3.00/libsrc/hdf_convenience.h +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.h ++++ libminc-2.3.00/libsrc/hdf_convenience.h +@@ -49,4 +49,5 @@ extern int hdf_open(const char *path, in + extern int hdf_create(const char *path, int mode, struct mi2opts *opts_ptr); + extern int hdf_close(int fd); + extern int hdf_access(const char *path); ++extern int hdf_flush(int fd); + +Index: libminc-2.3.00/libsrc/minc_compat.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/minc_compat.c ++++ libminc-2.3.00/libsrc/minc_compat.c +@@ -358,14 +358,9 @@ MI2redef(int fd) + MNCAPI int + MI2sync(int fd) + { +- if (MI2_ISH5OBJ(fd)) { ++ if (MI2_ISH5OBJ(fd) ) { + /* Commit the (entire) file to disk. */ +- if (H5Fflush(fd, H5F_SCOPE_GLOBAL) < 0) { +- return (MI_ERROR); +- } +- else { +- return (MI_NOERROR); +- } ++ return hdf_flush(fd); + } + else { + return (ncsync(fd)); +Index: libminc-2.3.00/libsrc/minc.h +=================================================================== +--- libminc-2.3.00.orig/libsrc/minc.h ++++ libminc-2.3.00/libsrc/minc.h +@@ -617,7 +617,13 @@ struct mi2opts { + int chunk_param; + }; + +-#define MI2_ISH5OBJ(x) (H5Iget_type(x) > 0) ++/* This is hackish in that it assumes that all NetCDF handles returned ++ * by ncopen/nccreate will be small integers. Historically this is ++ * true, but it could break someday. We used to use an HDF5 call, but ++ * that broke when HDF5 switched from 32 to 64 bits for hid_t. ++ */ ++#define HDF5_ID_MIN 0x30000000 ++#define MI2_ISH5OBJ(x) (x >= HDF5_ID_MIN) + + MNCAPI int micreatex(const char *path, int cmode, struct mi2opts *opts_ptr); + diff -Nru libminc-2.3.00/debian/patches/libhdf5-1.10.patch libminc-2.3.00/debian/patches/libhdf5-1.10.patch --- libminc-2.3.00/debian/patches/libhdf5-1.10.patch 1970-01-01 01:00:00.000000000 +0100 +++ libminc-2.3.00/debian/patches/libhdf5-1.10.patch 2016-10-20 19:29:50.000000000 +0200 @@ -0,0 +1,26 @@ +Index: libminc-2.3.00/libsrc/hdf_convenience.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.c ++++ libminc-2.3.00/libsrc/hdf_convenience.c +@@ -74,7 +74,7 @@ hdf_id_check(int fd) + } + + static struct m2_file * +-hdf_id_add(int fd) ++hdf_id_add(hid_t fd) + { + struct m2_file *new; + +Index: libminc-2.3.00/libsrc/netcdf_convenience.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/netcdf_convenience.c ++++ libminc-2.3.00/libsrc/netcdf_convenience.c +@@ -595,7 +595,7 @@ MNCAPI int miopen(const char *path, int + #if MINC2 + MNCAPI int micreatex(const char *path, int cmode, struct mi2opts *opts_ptr) + { +- int fd; ++ hid_t fd; + + MI_SAVE_ROUTINE_NAME("micreate"); + diff -Nru libminc-2.3.00/debian/patches/series libminc-2.3.00/debian/patches/series --- libminc-2.3.00/debian/patches/series 2016-08-25 15:25:30.000000000 +0200 +++ libminc-2.3.00/debian/patches/series 2016-10-20 20:26:41.000000000 +0200 @@ -3,3 +3,4 @@ use-system-nifti fix-endian-issues-label-data.patch Use-system-FindHDF5-CMake-module.patch +hdf5-1.10-support.patch diff -Nru libminc-2.3.00/debian/patches/upstream-92ba4fa.patch libminc-2.3.00/debian/patches/upstream-92ba4fa.patch --- libminc-2.3.00/debian/patches/upstream-92ba4fa.patch 1970-01-01 01:00:00.000000000 +0100 +++ libminc-2.3.00/debian/patches/upstream-92ba4fa.patch 2016-10-20 20:24:44.000000000 +0200 @@ -0,0 +1,70 @@ +From 92ba4fa2b8b88e02d5372b93a92a02f4e62385bc Mon Sep 17 00:00:00 2001 +From: "Vladimir S. FONOV" <vladimir.fo...@gmail.com> +Date: Thu, 8 Sep 2016 15:01:42 -0400 +Subject: [PATCH] Fixing function forgotten in + d99dd01632dbcb62870870557b333142b9117e9a , related to #74 + +--- + libsrc/hdf_convenience.c | 18 ++++++++++++++++++ + libsrc/hdf_convenience.h | 1 + + libsrc/minc_compat.c | 9 ++------- + 3 files changed, 21 insertions(+), 7 deletions(-) + +Index: libminc-2.3.00/libsrc/hdf_convenience.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.c ++++ libminc-2.3.00/libsrc/hdf_convenience.c +@@ -2412,4 +2412,22 @@ hdf_access(const char *path) + return (status > 0); /* Return non-zero if success */ + } + ++/* ++ * Flushes the hdf file to disk ++ */ ++int ++hdf_flush(int fd) ++{ ++ struct m2_file *file; ++ if ((file = hdf_id_check(fd))!=NULL ) { ++ /* Commit the (entire) file to disk. */ ++ if (H5Fflush(file->file_id, H5F_SCOPE_GLOBAL) < 0) { ++ return MI_ERROR; ++ } ++ return MI_NOERROR; ++ } ++ return MI_ERROR; ++} ++ ++ + #endif /* MINC2 defined */ +Index: libminc-2.3.00/libsrc/hdf_convenience.h +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.h ++++ libminc-2.3.00/libsrc/hdf_convenience.h +@@ -49,4 +49,5 @@ extern int hdf_open(const char *path, in + extern int hdf_create(const char *path, int mode, struct mi2opts *opts_ptr); + extern int hdf_close(int fd); + extern int hdf_access(const char *path); ++extern int hdf_flush(int fd); + +Index: libminc-2.3.00/libsrc/minc_compat.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/minc_compat.c ++++ libminc-2.3.00/libsrc/minc_compat.c +@@ -358,14 +358,9 @@ MI2redef(int fd) + MNCAPI int + MI2sync(int fd) + { +- if (MI2_ISH5OBJ(fd)) { ++ if (MI2_ISH5OBJ(fd) ) { + /* Commit the (entire) file to disk. */ +- if (H5Fflush(fd, H5F_SCOPE_GLOBAL) < 0) { +- return (MI_ERROR); +- } +- else { +- return (MI_NOERROR); +- } ++ return hdf_flush(fd); + } + else { + return (ncsync(fd)); diff -Nru libminc-2.3.00/debian/patches/upstream-d99dd01.patch libminc-2.3.00/debian/patches/upstream-d99dd01.patch --- libminc-2.3.00/debian/patches/upstream-d99dd01.patch 1970-01-01 01:00:00.000000000 +0100 +++ libminc-2.3.00/debian/patches/upstream-d99dd01.patch 2016-10-20 20:24:12.000000000 +0200 @@ -0,0 +1,402 @@ +From d99dd01632dbcb62870870557b333142b9117e9a Mon Sep 17 00:00:00 2001 +From: "Robert D. Vincent" <robert.d.vinc...@mcgill.ca> +Date: Wed, 27 Jul 2016 08:15:04 -0400 +Subject: [PATCH] Fix #74, don't assume hid_t === int since this is no longer + true in HDF5 1.10. + +--- + libsrc/hdf_convenience.c | 121 +++++++++++++++++++++++++---------------------- + libsrc/minc.h | 8 +++- + 2 files changed, 71 insertions(+), 58 deletions(-) + +Index: libminc-2.3.00/libsrc/hdf_convenience.c +=================================================================== +--- libminc-2.3.00.orig/libsrc/hdf_convenience.c ++++ libminc-2.3.00/libsrc/hdf_convenience.c +@@ -45,7 +45,8 @@ struct m2_dim { + + static struct m2_file { + struct m2_file *link; +- hid_t fd; ++ int fd; /* our fake file id */ ++ hid_t file_id; /* actual hdf5 file id */ + int wr_ok; /* non-zero if write OK */ + int resolution; /* Resolution setting. */ + int nvars; +@@ -74,18 +75,20 @@ hdf_id_check(int fd) + } + + static struct m2_file * +-hdf_id_add(int fd) ++hdf_id_add(hid_t file_id) + { + struct m2_file *new; ++ static unsigned short _id = 0; /* at most 2^16 id's */ + + new = (struct m2_file *) malloc(sizeof (struct m2_file)); + if (new != NULL) { +- new->fd = fd; ++ new->fd = HDF5_ID_MIN + _id++; ++ new->file_id = file_id; + new->resolution = 0; + new->nvars = 0; + new->ndims = 0; + new->link =_m2_list; +- new->grp_id = H5Gopen1(fd, MI2_GRPNAME); ++ new->grp_id = H5Gopen1(file_id, MI2_GRPNAME); + new->comp_type = MI2_COMP_UNKNOWN; + new->comp_param = 0; + new->chunk_type = MI2_CHUNK_UNKNOWN; +@@ -99,7 +102,7 @@ hdf_id_add(int fd) + return (new); + } + +-static int ++static int + hdf_id_del(int fd) + { + struct m2_file *curr, *prev; +@@ -142,6 +145,7 @@ hdf_id_del(int fd) + } + + H5Gclose(curr->grp_id); ++ H5Fclose(curr->file_id); + free(curr); + return (MI_NOERROR); + } +@@ -187,7 +191,7 @@ hdf_var_add(struct m2_file *file, const + strncpy(new->name, name, NC_MAX_NAME - 1); + strncpy(new->path, path, NC_MAX_NAME - 1); + new->is_cmpd = 0; +- new->dset_id = H5Dopen1(file->fd, path); ++ new->dset_id = H5Dopen1(file->file_id, path); + new->ftyp_id = H5Dget_type(new->dset_id); + new->mtyp_id = H5Tget_native_type(new->ftyp_id, H5T_DIR_ASCEND); + new->fspc_id = H5Dget_space(new->dset_id); +@@ -490,7 +494,7 @@ hdf_attinq(int fd, int varid, const char + return (MI_ERROR); + } + +- if (varid == NC_GLOBAL) { ++ if (varid == NC_GLOBAL || varid == MI_ROOTVARIABLE_ID) { + var = NULL; + loc_id = file->grp_id; + } +@@ -591,7 +595,7 @@ hdf_attinq(int fd, int varid, const char + } + + static int +-hdf_put_dimorder(struct m2_file *file, int dst_id, int ndims, ++hdf_put_dimorder(struct m2_file *file, hid_t dst_id, int ndims, + const int *dims_ptr) + { + int i; +@@ -626,6 +630,9 @@ hdf_put_dimorder(struct m2_file *file, i + if (att_id >= 0) { + H5Awrite(att_id, typ_id, str_buf); + } ++ else { ++ fprintf(stderr, "Failed to create dimorder %lx\n", dst_id); ++ } + + H5Aclose(att_id); + H5Sclose(spc_id); +@@ -634,7 +641,7 @@ hdf_put_dimorder(struct m2_file *file, i + } + + static int +-hdf_get_dimorder(struct m2_file *file, int dst_id, int ndims, int *dims_ptr) ++hdf_get_dimorder(struct m2_file *file, hid_t dst_id, int ndims, int *dims_ptr) + { + char *str_ptr; + char *tmp_ptr; +@@ -974,7 +981,7 @@ hdf_attget(int fd, int varid, const char + return (MI_ERROR); + } + +- if (varid == NC_GLOBAL) { ++ if (varid == NC_GLOBAL || varid == MI_ROOTVARIABLE_ID) { + var = NULL; + loc_id = file->grp_id; + } +@@ -1120,11 +1127,11 @@ hdf_attput(int fd, int varid, const char + H5Pclose(new_plst_id); + H5Sclose(var->fspc_id); + +- if (H5Gunlink(fd, var->path) < 0) { ++ if (H5Gunlink(file->file_id, var->path) < 0) { + milog_message(MI_MSG_SNH); + } + +- if (H5Gmove2(file->grp_id, temp, fd, var->path) < 0) { ++ if (H5Gmove2(file->grp_id, temp, file->file_id, var->path) < 0) { + milog_message(MI_MSG_SNH); + } + +@@ -1196,7 +1203,7 @@ hdf_attput(int fd, int varid, const char + att_id = H5Acreate2(loc_id, attnm, ftyp_id, spc_id, H5P_DEFAULT, H5P_DEFAULT); + + if (att_id < 0) +- goto cleanup; ++ goto cleanup; + + /* Save the value. + */ +@@ -1261,10 +1268,10 @@ int + hdf_vardef(int fd, const char *varnm, nc_type vartype, int ndims, + const int *dimids) + { +- int dst_id = -1; +- int typ_id = -1; +- int spc_id = -1; +- int prp_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t spc_id = -1; ++ hid_t prp_id = -1; + int status = MI_ERROR; + int i; + long length; +@@ -1392,7 +1399,7 @@ hdf_vardef(int fd, const char *varnm, nc + } + + H5E_BEGIN_TRY { +- dst_id = H5Dcreate2(fd, varpath, typ_id, spc_id, H5P_DEFAULT, prp_id, H5P_DEFAULT); ++ dst_id = H5Dcreate2(file->file_id, varpath, typ_id, spc_id, H5P_DEFAULT, prp_id, H5P_DEFAULT); + } H5E_END_TRY; + + if (dst_id < 0) { +@@ -1465,10 +1472,10 @@ hdf_varget(int fd, int varid, const long + void *val_ptr) + { + int status = MI_ERROR; +- int dst_id = -1; +- int typ_id = -1; +- int fspc_id = -1; +- int mspc_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t fspc_id = -1; ++ hid_t mspc_id = -1; + int i; + int ndims; + hsize_t fstart[MAX_VAR_DIMS]; +@@ -1560,8 +1567,8 @@ hdf_varget(int fd, int varid, const long + } + + int +-hdf_varputg(int fd, int varid, const long *start, +- const long *edges, const long *stride, ++hdf_varputg(int fd, int varid, const long *start, ++ const long *edges, const long *stride, + const long *map, const void *value) + { + int status = MI_ERROR; /* Assume guilty */ +@@ -1577,10 +1584,10 @@ hdf_varputg(int fd, int varid, const lon + + struct m2_var *varp; + struct m2_file *file; +- int dst_id = -1; +- int typ_id = -1; +- int fspc_id = -1; +- int mspc_id = -1; ++ hid_t dst_id = -1; ++ hid_t typ_id = -1; ++ hid_t fspc_id = -1; ++ hid_t mspc_id = -1; + + if ((file = hdf_id_check(fd)) == NULL) { + return (MI_ERROR); +@@ -1747,8 +1754,8 @@ hdf_varputg(int fd, int varid, const lon + } + + int +-hdf_vargetg(int fd, int varid, const long *start, +- const long *edges, const long *stride, ++hdf_vargetg(int fd, int varid, const long *start, ++ const long *edges, const long *stride, + const long *map, void *value) + { + int status = MI_NOERROR; +@@ -1910,10 +1917,10 @@ hdf_varput(int fd, int varid, const long + const void *val_ptr) + { + int status = MI_ERROR; +- int dst_id; +- int typ_id; +- int fspc_id; +- int mspc_id = -1; ++ hid_t dst_id; ++ hid_t typ_id; ++ hid_t fspc_id; ++ hid_t mspc_id = -1; + int i; + int ndims; + hsize_t fstart[MAX_VAR_DIMS]; +@@ -2085,6 +2092,7 @@ herr_t hdf_copy_attr(hid_t in_id, const + * don't overwrite the existing value. + */ + status = MI_NOERROR; ++ fprintf(stderr, "Failed to create attribute '%s'\n", attr_name); + goto cleanup; + } + +@@ -2195,7 +2203,7 @@ hdf_open_dsets(struct m2_file *file, hid + int + hdf_open(const char *path, int mode) + { +- hid_t fd; ++ hid_t file_id; + hid_t grp_id; + hid_t dset_id; + struct m2_file *file; +@@ -2210,28 +2218,28 @@ hdf_open(const char *path, int mode) + + prp_id = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mmap(prp_id, 8192, 1); +- fd = H5Fopen(path, mode & 0x7FFF, prp_id); ++ file_id = H5Fopen(path, mode & 0x7FFF, prp_id); + H5Pclose(prp_id); + } + else { +- fd = H5Fopen(path, mode, H5P_DEFAULT); ++ file_id = H5Fopen(path, mode, H5P_DEFAULT); + } + #else +- fd = H5Fopen(path, mode, H5P_DEFAULT); ++ file_id = H5Fopen(path, mode, H5P_DEFAULT); + #endif + } H5E_END_TRY; + +- if (fd < 0) { ++ if (file_id < 0) { + return (MI_ERROR); + } + +- file = hdf_id_add(fd); /* Add it to the list */ ++ file = hdf_id_add(file_id); /* Add it to the list */ + file->wr_ok = (mode & H5F_ACC_RDWR) != 0; + + /* Open the image variables. + */ + H5E_BEGIN_TRY { +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image"); + if (dset_id >= 0) { + hid_t type_id; + int is_compound = 0; +@@ -2262,7 +2270,7 @@ hdf_open(const char *path, int mode) + H5Dclose(dset_id); + } + +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image-min"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image-min"); + if (dset_id >= 0) { + hdf_get_diminfo(dset_id, &ndims, dims); + hdf_var_add(file, MIimagemin, "/minc-2.0/image/0/image-min", +@@ -2270,7 +2278,7 @@ hdf_open(const char *path, int mode) + H5Dclose(dset_id); + } + +- dset_id = H5Dopen1(fd, "/minc-2.0/image/0/image-max"); ++ dset_id = H5Dopen1(file_id, "/minc-2.0/image/0/image-max"); + if (dset_id >= 0) { + hdf_get_diminfo(dset_id, &ndims, dims); + hdf_var_add(file, MIimagemax, "/minc-2.0/image/0/image-max", +@@ -2281,16 +2289,16 @@ hdf_open(const char *path, int mode) + + /* Open all of the datasets in the "dimensions" category. + */ +- grp_id = H5Gopen2(fd, "/minc-2.0/dimensions", H5P_DEFAULT); ++ grp_id = H5Gopen2(file_id, "/minc-2.0/dimensions", H5P_DEFAULT); + hdf_open_dsets(file, grp_id, "/minc-2.0/dimensions/", 1); + H5Gclose(grp_id); + + /* Open all of the datasets in the "info" category. + */ +- grp_id = H5Gopen2(fd, "/minc-2.0/info", H5P_DEFAULT); ++ grp_id = H5Gopen2(file_id, "/minc-2.0/info", H5P_DEFAULT); + hdf_open_dsets(file, grp_id, "/minc-2.0/info/", 0); + H5Gclose(grp_id); +- return (fd); ++ return (file->fd); + } + + /** Create an HDF5 file. */ +@@ -2298,7 +2306,7 @@ int + hdf_create(const char *path, int cmode, struct mi2opts *opts_ptr) + { + hid_t grp_id; +- hid_t fd; ++ hid_t file_id; + hid_t tmp_id; + struct m2_file *file; + hid_t hdf_gpid; +@@ -2319,10 +2327,10 @@ hdf_create(const char *path, int cmode, + H5Pset_libver_bounds (fpid, H5F_LIBVER_18, H5F_LIBVER_18); + + H5E_BEGIN_TRY { +- fd = H5Fcreate(path, cmode, H5P_DEFAULT, fpid); ++ file_id = H5Fcreate(path, cmode, H5P_DEFAULT, fpid); + } H5E_END_TRY; +- if (fd < 0) { +- fprintf(stderr, "Error creating HDF file '%s' with mode '%x', result %d\n", path, cmode, fd); ++ if (file_id < 0) { ++ fprintf(stderr, "Error creating HDF file '%s' with mode '%x', result %d\n", path, cmode, (int)file_id); + H5Eprint1(stderr); + return (MI_ERROR); + } +@@ -2332,7 +2340,7 @@ hdf_create(const char *path, int cmode, + /* Create the default groups. + * Should we use a non-zero value for size_hint (parameter 3)??? + */ +- if ((grp_id = H5Gcreate2(fd, MI2_GRPNAME, H5P_DEFAULT, hdf_gpid, H5P_DEFAULT)) < 0) { ++ if ((grp_id = H5Gcreate2(file_id, MI2_GRPNAME, H5P_DEFAULT, hdf_gpid, H5P_DEFAULT)) < 0) { + fprintf(stderr, "Error creating groups on line %d\n", __LINE__); + H5Eprint1(stderr); + return (MI_ERROR); +@@ -2369,7 +2377,7 @@ hdf_create(const char *path, int cmode, + H5Gclose(tmp_id); + H5Gclose(grp_id); + +- file = hdf_id_add(fd); /* Add it to the list */ ++ file = hdf_id_add(file_id); /* Add it to the list */ + if (file == NULL) { + fprintf(stderr, "Error adding ID to list.\n"); + H5Eprint1(stderr); +@@ -2384,7 +2392,7 @@ hdf_create(const char *path, int cmode, + file->chunk_type = opts_ptr->chunk_type; + file->chunk_param = opts_ptr->chunk_param; + } +- return ((int) fd); ++ return (file->fd); + } + + int +@@ -2392,7 +2400,6 @@ hdf_close(int fd) + { + hdf_dim_commit(fd); /* Make sure all dimensions were saved. */ + hdf_id_del(fd); /* Delete it from the list. */ +- H5Fclose(fd); + return (MI_NOERROR); + } + +Index: libminc-2.3.00/libsrc/minc.h +=================================================================== +--- libminc-2.3.00.orig/libsrc/minc.h ++++ libminc-2.3.00/libsrc/minc.h +@@ -617,7 +617,13 @@ struct mi2opts { + int chunk_param; + }; + +-#define MI2_ISH5OBJ(x) (H5Iget_type(x) > 0) ++/* This is hackish in that it assumes that all NetCDF handles returned ++ * by ncopen/nccreate will be small integers. Historically this is ++ * true, but it could break someday. We used to use an HDF5 call, but ++ * that broke when HDF5 switched from 32 to 64 bits for hid_t. ++ */ ++#define HDF5_ID_MIN 0x30000000 ++#define MI2_ISH5OBJ(x) (x >= HDF5_ID_MIN) + + MNCAPI int micreatex(const char *path, int cmode, struct mi2opts *opts_ptr); + diff -Nru libminc-2.3.00/debian/rules libminc-2.3.00/debian/rules --- libminc-2.3.00/debian/rules 2015-09-05 08:03:54.000000000 +0200 +++ libminc-2.3.00/debian/rules 2016-10-20 19:29:50.000000000 +0200 @@ -1,5 +1,6 @@ #! /usr/bin/make -f +export DEB_CPPFLAGS_MAINT_APPEND := -Wconversion ARCH = $(shell dpkg-architecture -qDEB_TARGET_MULTIARCH)
