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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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Can't install HDF5Array_1.19.3 in R 4.1.0 #35

Closed dpelegri closed 3 years ago

dpelegri commented 3 years ago

Hello,

I can't install HDF5Array_1.19.3 from source in R 4.1.0, I get the error,

lzf/lzf/lzf_c.c:124:19: error: expected '=', ',', ';', 'asm' or 'attribute' before 'off' unsigned _int64 off; / workaround for missing POSIX compliance /

My system is a Wk7 and the output is :

` install.packages("C:/Users/Administrator/Downloads/HDF5Array_1.19.3.tar.gz", repos = NULL, type = "source")

*** arch - i386 /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lzf/lzf/lzf_c.c -o lzf/lzf/lzf_c.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lzf/lzf/lzf_d.c -o lzf/lzf/lzf_d.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lzf/lzf_filter.c -o lzf/lzf_filter.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c global_errmsg_buf.c -o global_errmsg_buf.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c uaselection.c -o uaselection.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5DSetDescriptor.c -o H5DSetDescriptor.o In file included from H5DSetDescriptor.c:7: H5DSetDescriptor.c: In function 'map_native_type_to_predef_type': H5DSetDescriptor.c:82:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'hid_t' {aka 'long long int'} [-Wformat=] PRINT_TO_ERRMSG_BUF("failed to map native type id %ld " ^~~~~~~~~~~ "to predef type id", native_type_id);

global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
H5DSetDescriptor.c:82:54: note: format string is defined here
  PRINT_TO_ERRMSG_BUF("failed to map native type id %ld "
                                                    ~~^
                                                    %I64d
H5DSetDescriptor.c: In function 'predef_native_type_as_string':
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_helpers.c -o h5mread_helpers.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_startscounts.c -o h5mread_startscounts.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChunkIterator.c -o ChunkIterator.o
In file included from ChunkIterator.c:7:
ChunkIterator.c: In function 'read_h5chunk':
ChunkIterator.c:326:23: warning: unknown conversion type character 'l' in format [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:326:46: note: format string is defined here
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                                              ^
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ChunkIterator.c:328:9:
         chunk_storage_size,

global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, VA_ARGS) ^~~ ChunkIterator.c:327:27: note: format string is defined here "than expected (%lu + %d)", ~~^ %I64u In file included from ChunkIterator.c:7: ChunkIterator.c:326:23: warning: too many arguments for format [-Wformat-extra-args] PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger " ^~~~~~~~~~~ global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, VA_ARGS) ^~~ /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_index.c -o h5mread_index.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_sparse.c -o h5mread_sparse.o h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function] static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE nzindex_bufs, ^~~~~~~ h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function] static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE nzdata_bufs, ^~~~~~~~ h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function] static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf, ^~~~~~~~~~ /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5summarize.c -o h5summarize.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5dimscales.c -o h5dimscales.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_HDF5Array.c -o R_init_HDF5Array.o /mingw32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def lzf/lzf/lzf_c.o lzf/lzf/lzf_d.o lzf/lzf_filter.o S4Vectors_stubs.o global_errmsg_buf.o uaselection.o H5DSetDescriptor.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o h5dimscales.o R_init_HDF5Array.o -LC:/PROGRA~1/R/R-devel/library/Rhdf5lib/lib/i386 -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/PROGRA~1/R/R-devel/bin/i386 -lR installing to C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/libs/i386

arch - x64 /mingw64/bin/gcc -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lzf/lzf/lzf_c.c -o lzf/lzf/lzf_c.o lzf/lzf/lzf_c.c: In function 'lzf_compress': lzf/lzf/lzf_c.c:124:19: error: expected '=', ',', ';', 'asm' or 'attribute' before 'off' unsigned _int64 off; / workaround for missing POSIX compliance / ^~~ lzf/lzf/lzf_c.c:124:19: error: 'off' undeclared (first use in this function) lzf/lzf/lzf_c.c:124:19: note: each undeclared identifier is reported only once for each function it appears in make: [C:/PROGRA~1/R/R-devel/etc/x64/Makeconf:237: lzf/lzf/lzf_c.o] Error 1 ERROR: compilation failed for package 'HDF5Array'

My sessionInfo :

`>sessionInfo() R Under development (unstable) (2021-02-10 r79988) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C LC_TIME=Spanish_Spain.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.10 compiler_4.1.0 tools_4.1.0 `

Thanks

Dolors

dpelegri commented 3 years ago

Hi,

I try to install the new version 1.19.4 and now I get a new error related to : arch - i386 my system is W7 x64. I send the full installation report.

Thanks,

Dolors

>install.packages("C:/Users/Administrator/Downloads/HDF5Array_1.19.4.tar.gz", repos = NULL, type = "source")
* installing *source* package 'HDF5Array' ...
** using staged installation
** libs

*** arch - i386
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf/lzf_c.c -o lzf/lzf/lzf_c.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf/lzf_d.c -o lzf/lzf/lzf_d.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf_filter.c -o lzf/lzf_filter.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c global_errmsg_buf.c -o global_errmsg_buf.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c uaselection.c -o uaselection.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
In file included from H5DSetDescriptor.c:7:
H5DSetDescriptor.c: In function 'map_native_type_to_predef_type':
H5DSetDescriptor.c:82:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  PRINT_TO_ERRMSG_BUF("failed to map native type id %ld "
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        "to predef type id", native_type_id);
                             ~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
H5DSetDescriptor.c:82:54: note: format string is defined here
  PRINT_TO_ERRMSG_BUF("failed to map native type id %ld "
                                                    ~~^
                                                    %I64d
H5DSetDescriptor.c: In function 'predef_native_type_as_string':
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_helpers.c -o h5mread_helpers.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_startscounts.c -o h5mread_startscounts.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChunkIterator.c -o ChunkIterator.o
In file included from ChunkIterator.c:7:
ChunkIterator.c: In function 'read_h5chunk':
ChunkIterator.c:326:23: warning: unknown conversion type character 'l' in format [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:326:46: note: format string is defined here
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                                              ^
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ChunkIterator.c:328:9:
         chunk_storage_size,
         ~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:327:27: note: format string is defined here
         "than expected (%lu + %d)",
                         ~~^
                         %I64u
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: too many arguments for format [-Wformat-extra-args]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_index.c -o h5mread_index.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread.c -o h5mread.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5summarize.c -o h5summarize.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5dimscales.c -o h5dimscales.o
/mingw32/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
/mingw32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def lzf/lzf/lzf_c.o lzf/lzf/lzf_d.o lzf/lzf_filter.o S4Vectors_stubs.o global_errmsg_buf.o uaselection.o H5DSetDescriptor.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o h5dimscales.o R_init_HDF5Array.o -LC:/PROGRA~1/R/R-devel/library/Rhdf5lib/lib/i386 -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/PROGRA~1/R/R-devel/bin/i386 -lR
installing to C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/libs/i386

*** arch - x64
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf/lzf_c.c -o lzf/lzf/lzf_c.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf/lzf_d.c -o lzf/lzf/lzf_d.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lzf/lzf_filter.c -o lzf/lzf_filter.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c global_errmsg_buf.c -o global_errmsg_buf.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c uaselection.c -o uaselection.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
In file included from H5DSetDescriptor.c:7:
H5DSetDescriptor.c: In function 'map_native_type_to_predef_type':
H5DSetDescriptor.c:82:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  PRINT_TO_ERRMSG_BUF("failed to map native type id %ld "
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        "to predef type id", native_type_id);
                             ~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
H5DSetDescriptor.c:82:54: note: format string is defined here
  PRINT_TO_ERRMSG_BUF("failed to map native type id %ld "
                                                    ~~^
                                                    %I64d
H5DSetDescriptor.c: In function 'predef_native_type_as_string':
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
H5DSetDescriptor.c:155:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  sprintf(s, "unknown native type (%ld)", native_type_id);
                                   ~~^    ~~~~~~~~~~~~~~
                                   %I64d
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_helpers.c -o h5mread_helpers.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_startscounts.c -o h5mread_startscounts.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChunkIterator.c -o ChunkIterator.o
In file included from ChunkIterator.c:7:
ChunkIterator.c: In function 'read_h5chunk':
ChunkIterator.c:326:23: warning: unknown conversion type character 'l' in format [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:326:46: note: format string is defined here
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                                              ^
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ChunkIterator.c:328:9:
         chunk_storage_size,
         ~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:327:27: note: format string is defined here
         "than expected (%lu + %d)",
                         ~~^
                         %I64u
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: format '%d' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ChunkIterator.c:329:9:
         chunk_data_buf->data_size,
         ~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
ChunkIterator.c:327:32: note: format string is defined here
         "than expected (%lu + %d)",
                               ~^
                               %I64d
In file included from ChunkIterator.c:7:
ChunkIterator.c:326:23: warning: too many arguments for format [-Wformat-extra-args]
   PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
  snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
                                                              ^~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_index.c -o h5mread_index.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
 static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5mread.c -o h5mread.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5summarize.c -o h5summarize.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c h5dimscales.c -o h5dimscales.o
/mingw64/bin/gcc  -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG -Ilzf/lzf -I'C:/Program Files/R/R-devel/library/S4Vectors/include' -I'C:/Program Files/R/R-devel/library/Rhdf5lib/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
/mingw64/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def lzf/lzf/lzf_c.o lzf/lzf/lzf_d.o lzf/lzf_filter.o S4Vectors_stubs.o global_errmsg_buf.o uaselection.o H5DSetDescriptor.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o h5dimscales.o R_init_HDF5Array.o -LC:/PROGRA~1/R/R-devel/library/Rhdf5lib/lib/x64 -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/PROGRA~1/R/R-devel/bin/x64 -lR
installing to C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HDF5Array'
    finding HTML links ... done
    H5ADMatrix-class                        html  
REDIRECT:topic   class:H5ADMatrix -> H5ADMatrix-class.html [ FAIL ]
REDIRECT:topic   H5ADMatrix-class -> H5ADMatrix-class.html [ SUCCESS ]
REDIRECT:topic   H5ADMatrix -> H5ADMatrix-class.html [ SUCCESS ]
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REDIRECT:topic   read_sparse_block,H5ADMatrix-method -> H5ADMatrix-class.html [ SUCCESS ]
REDIRECT:topic   extractNonzeroDataByCol,H5ADMatrix-method -> H5ADMatrix-class.html [ SUCCESS ]
REDIRECT:topic   coerce,H5ADMatrix,dgCMatrix-method -> H5ADMatrix-class.html [ SUCCESS ]
REDIRECT:topic   coerce,H5ADMatrix,sparseMatrix-method -> H5ADMatrix-class.html [ SUCCESS ]
    H5ADMatrixSeed-class                    html  
REDIRECT:topic   class:Dense_H5ADMatrixSeed -> H5ADMatrixSeed-class.html [ FAIL ]
REDIRECT:topic   Dense_H5ADMatrixSeed-class -> H5ADMatrixSeed-class.html [ SUCCESS ]
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    H5SparseMatrixSeed-class                html  
REDIRECT:topic   class:H5SparseMatrixSeed -> H5SparseMatrixSeed-class.html [ FAIL ]
REDIRECT:topic   H5SparseMatrixSeed-class -> H5SparseMatrixSeed-class.html [ SUCCESS ]
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REDIRECT:topic   read_sparse_block,H5SparseMatrixSeed-method -> H5SparseMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   extractNonzeroDataByCol -> H5SparseMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   extractNonzeroDataByCol,H5SparseMatrixSeed-method -> H5SparseMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   coerce,H5SparseMatrixSeed,dgCMatrix-method -> H5SparseMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   coerce,H5SparseMatrixSeed,sparseMatrix-method -> H5SparseMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   show,H5SparseMatrixSeed-method -> H5SparseMatrixSeed-class.html [ SUCCESS ]
Rd warning: no fue posible abrir el archivo 'C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/help/path<-,H5SparseMatrixSeed-method.html': Invalid argument
    HDF5Array-class                         html  
REDIRECT:topic   class:HDF5Array -> HDF5Array-class.html [ FAIL ]
REDIRECT:topic   HDF5Array-class -> HDF5Array-class.html [ SUCCESS ]
REDIRECT:topic   HDF5Array -> HDF5Array-class.html [ SUCCESS ]
REDIRECT:topic   DelayedArray,HDF5ArraySeed-method -> HDF5Array-class.html [ SUCCESS ]
REDIRECT:topic   class:HDF5Matrix -> HDF5Array-class.html [ FAIL ]
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REDIRECT:topic   matrixClass,HDF5Array-method -> HDF5Array-class.html [ SUCCESS ]
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Rd warning: no fue posible abrir el archivo 'C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/help/is_sparse<-,HDF5Array-method.html': Invalid argument
    HDF5ArraySeed-class                     html  
REDIRECT:topic   class:HDF5ArraySeed -> HDF5ArraySeed-class.html [ FAIL ]
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REDIRECT:topic   extract_array,HDF5ArraySeed-method -> HDF5ArraySeed-class.html [ SUCCESS ]
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REDIRECT:topic   extract_sparse_array,HDF5ArraySeed-method -> HDF5ArraySeed-class.html [ SUCCESS ]
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REDIRECT:topic   updateObject,HDF5ArraySeed-method -> HDF5ArraySeed-class.html [ SUCCESS ]
Rd warning: no fue posible abrir el archivo 'C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/help/path<-,HDF5ArraySeed-method.html': Invalid argument
Rd warning: no fue posible abrir el archivo 'C:/Program Files/R/R-devel/library/00LOCK-HDF5Array/00new/HDF5Array/help/is_sparse<-,HDF5ArraySeed-method.html': Invalid argument
    ReshapedHDF5Array-class                 html  
REDIRECT:topic   class:ReshapedHDF5Array -> ReshapedHDF5Array-class.html [ FAIL ]
REDIRECT:topic   ReshapedHDF5Array-class -> ReshapedHDF5Array-class.html [ SUCCESS ]
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REDIRECT:topic   coerce,ReshapedHDF5Array,ReshapedHDF5Matrix-method -> ReshapedHDF5Array-class.html [ SUCCESS ]
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    ReshapedHDF5ArraySeed-class             html  
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    TENxMatrix-class                        html  
REDIRECT:topic   class:TENxMatrix -> TENxMatrix-class.html [ FAIL ]
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    TENxMatrixSeed-class                    html  
REDIRECT:topic   class:TENxMatrixSeed -> TENxMatrixSeed-class.html [ FAIL ]
REDIRECT:topic   TENxMatrixSeed-class -> TENxMatrixSeed-class.html [ SUCCESS ]
REDIRECT:topic   TENxMatrixSeed -> TENxMatrixSeed-class.html [ SUCCESS ]
    dump-management                         html  
REDIRECT:topic   HDF5-dump-management -> dump-management.html [ SUCCESS ]
REDIRECT:topic   dump-management -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpDir -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpDir -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpFile -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpFile -> dump-management.html [ SUCCESS ]
REDIRECT:topic   lsHDF5DumpFile -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpName -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpName -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpChunkLength -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpChunkLength -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpChunkShape -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpChunkShape -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpChunkDim -> dump-management.html [ SUCCESS ]
REDIRECT:topic   setHDF5DumpCompressionLevel -> dump-management.html [ SUCCESS ]
REDIRECT:topic   getHDF5DumpCompressionLevel -> dump-management.html [ SUCCESS ]
REDIRECT:topic   appendDatasetCreationToHDF5DumpLog -> dump-management.html [ SUCCESS ]
REDIRECT:topic   showHDF5DumpLog -> dump-management.html [ SUCCESS ]
    finding level-2 HTML links ... done

    h5mread                                 html  
REDIRECT:topic   class:H5DSetDescriptor -> h5mread.html [ FAIL ]
REDIRECT:topic   H5DSetDescriptor-class -> h5mread.html [ SUCCESS ]
REDIRECT:topic   H5DSetDescriptor -> h5mread.html [ SUCCESS ]
REDIRECT:topic   destroy_H5DSetDescriptor -> h5mread.html [ SUCCESS ]
REDIRECT:topic   show,H5DSetDescriptor-method -> h5mread.html [ SUCCESS ]
REDIRECT:topic   get_h5mread_returned_type -> h5mread.html [ SUCCESS ]
REDIRECT:topic   h5mread -> h5mread.html [ SUCCESS ]
    h5mread_from_reshaped                   html  
REDIRECT:topic   h5mread_from_reshaped -> h5mread_from_reshaped.html [ SUCCESS ]
    h5writeDimnames                         html  
REDIRECT:topic   h5writeDimnames -> h5writeDimnames.html [ SUCCESS ]
REDIRECT:topic   h5readDimnames -> h5writeDimnames.html [ SUCCESS ]
REDIRECT:topic   set_h5dimnames -> h5writeDimnames.html [ SUCCESS ]
REDIRECT:topic   get_h5dimnames -> h5writeDimnames.html [ SUCCESS ]
    saveHDF5SummarizedExperiment            html  
REDIRECT:topic   saveHDF5SummarizedExperiment -> saveHDF5SummarizedExperiment.html [ SUCCESS ]
REDIRECT:topic   quickResaveHDF5SummarizedExperiment -> saveHDF5SummarizedExperiment.html [ SUCCESS ]
REDIRECT:topic   loadHDF5SummarizedExperiment -> saveHDF5SummarizedExperiment.html [ SUCCESS ]
    writeHDF5Array                          html  
REDIRECT:topic   class:HDF5RealizationSink -> writeHDF5Array.html [ FAIL ]
REDIRECT:topic   HDF5RealizationSink-class -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   HDF5RealizationSink -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   dimnames,HDF5RealizationSink-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   type,HDF5RealizationSink-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   chunkdim,HDF5RealizationSink-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   is_sparse,HDF5RealizationSink-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   write_block,HDF5RealizationSink-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,HDF5RealizationSink,HDF5ArraySeed-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,HDF5RealizationSink,HDF5Array-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,HDF5RealizationSink,DelayedArray-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   writeHDF5Array -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,ANY,HDF5Array-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,DelayedArray,HDF5Array-method -> writeHDF5Array.html [ SUCCESS ]
REDIRECT:topic   coerce,DelayedMatrix,HDF5Matrix-method -> writeHDF5Array.html [ SUCCESS ]
    writeTENxMatrix                         html  
REDIRECT:topic   class:TENxRealizationSink -> writeTENxMatrix.html [ FAIL ]
REDIRECT:topic   TENxRealizationSink-class -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   TENxRealizationSink -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   dimnames,TENxRealizationSink-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   type,TENxRealizationSink-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   chunkdim,TENxRealizationSink-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   write_block,TENxRealizationSink-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   close,TENxRealizationSink-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,TENxRealizationSink,TENxMatrixSeed-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,TENxRealizationSink,TENxMatrix-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,TENxRealizationSink,DelayedArray-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   writeTENxMatrix -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,ANY,TENxMatrix-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,DelayedArray,TENxMatrix-method -> writeTENxMatrix.html [ SUCCESS ]
REDIRECT:topic   coerce,DelayedMatrix,TENxMatrix-method -> writeTENxMatrix.html [ SUCCESS ]
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error : package 'rhdf5' is not installed for 'arch = i386'
Error: loading failed
Ejecución interrumpida
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Program Files/R/R-devel/library/HDF5Array'
Warning in install.packages :
  installation of package ‘C:/Users/Administrator/Downloads/HDF5Array_1.19.4.tar.gz’ had non-zero exit status
hpages commented 3 years ago

I see:

Error : package 'rhdf5' is not installed for 'arch = i386'

So it looks like rhdf5 was only installed for the x64 arch. Not really an HDF5Array issue.

You have 2 options:

  1. Either make sure to install rhdf5 for both archs. If you struggle with this, please open an issue in the rdhf5 repo.

  2. Or install HDF5Array only for the x64 arch. You should be able to do this with something like:

    R --arch x64 CMD INSTALL --no-multiarch HDF5Array_1.19.4.tar.gz

    in a PowerShell.

dpelegri commented 3 years ago

Hi hpages,

You're right, I didn't notice that now the error package was an rhdf5 error, I installed rhdf5 2.35.2 and HDF5Array 1.19.4 and everything was ok in x64 and i386 arch .

Thanks a lot,

Dolors

hpages commented 3 years ago

Excellent! Glad it worked for you.