Installation error - libsz.so.2: cannot open shared object file: No such file or directory #65
Description
Hi,
I'm trying to install Rhdf5lib in a cluster. I tried R versions 4.3 (which is already installed in the server cluster), conda version 4.4.3 and docker version 4.5 - latest
In all versions, I'm getting the same error, as follows:
> BiocManager::install("Rhdf5lib")
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.3 (2025-02-28)
Installing package(s) 'Rhdf5lib'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/Rhdf5lib_1.28.0.tar.gz'
Content type 'application/gzip' length 12065121 bytes (11.5 MB)
==================================================
downloaded 11.5 MB
* installing *source* package ‘Rhdf5lib’ ...
** package ‘Rhdf5lib’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... x86_64-conda-linux-gnu-cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to enable C11 features... none needed
checking whether the compiler supports GNU C++... yes
checking whether x86_64-conda-linux-gnu-c++ -std=gnu++17 accepts -g... yes
checking for x86_64-conda-linux-gnu-c++ -std=gnu++17 option to enable C++11 features... none needed
COMPILER = x86_64-conda-linux-gnu-cc
checking whether to use -Wl,-rpath setting... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
ON_BUILDER=false
ON_BUILDER=false
checking for szlib.h... yes
checking for libaec.h... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for aec_buffer_encode in -lsz... yes
checking for curl/curl.h... yes
checking for openssl/evp.h... yes
checking for openssl/hmac.h... yes
checking for openssl/sha.h... yes
checking for curl_global_init in -lcurl... yes
checking for EVP_sha256 in -lcrypto... yes
S3_VFD=--enable-ros3-vfd
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 15.1.0-2) 15.1.0’
gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -;
cd hdf5; \
./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \
--enable-tests=no --enable-tools=no \
--with-szlib=yes --with-zlib=yes \
--enable-ros3-vfd \
--enable-sharedlib-rpath \
CC='x86_64-conda-linux-gnu-cc' CXX='x86_64-conda-linux-gnu-c++ -std=gnu++17' \
CPPFLAGS='-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -I/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib' \
CFLAGS='-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -fdebug-prefix-map=/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45=/usr/local/src/conda-prefix -fpic' \
CXXFLAGS='-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -fdebug-prefix-map=/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45=/usr/local/src/conda-prefix -fpic' \
AR='x86_64-conda-linux-gnu-ar' RANLIB='x86_64-conda-linux-gnu-ranlib' \
LDFLAGS='-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib'; \
make lib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-pc-linux-gnu... no
checking for config x86_64-pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-pc... no
checking for config linux-gnu... found
compiler 'x86_64-conda-linux-gnu-cc' is GNU gcc-15.1.0
compiler 'x86_64-conda-linux-gnu-gfortran' is GNU gfortran-15.1.0
compiler 'x86_64-conda-linux-gnu-c++ -std=gnu++17' is GNU g++-15.1.0
No match to get cc_version_info for x86_64-conda-linux-gnu-cc
No match to get cxx_version_info for x86_64-conda-linux-gnu-c++ -std=gnu++17
checking for config ./config/site-specific/host-c484... no
checking for clang sanitizer checks... checking build mode... production
checking for gcc... x86_64-conda-linux-gnu-cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to enable C11 features... none needed
checking whether x86_64-conda-linux-gnu-cc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of x86_64-conda-linux-gnu-cc... gcc3
checking if unsupported combinations of configure options are allowed... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... no
checking whether the compiler supports GNU C++... yes
checking whether x86_64-conda-linux-gnu-c++ -std=gnu++17 accepts -g... yes
checking for x86_64-conda-linux-gnu-c++ -std=gnu++17 option to enable C++11 features... none needed
checking dependency style of x86_64-conda-linux-gnu-c++ -std=gnu++17... gcc3
checking how to run the C++ preprocessor... x86_64-conda-linux-gnu-c++ -std=gnu++17 -E
checking if c++ interface enabled... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 needs old style header files in includes... no
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 can handle namespaces... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 can handle static cast... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 has offsetof extension... yes
checking if the high-level library is enabled... yes
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... yes
checking if Java JNI interface enabled... no
checking if building tests is disabled... Building HDF5 tests is disabled
checking if building tools is disabled... Building HDF5 tools is disabled
checking how to print strings... printf
checking for a sed that does not truncate output... /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by x86_64-conda-linux-gnu-cc... /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld
checking if the linker (/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... x86_64-conda-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from x86_64-conda-linux-gnu-cc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-conda-linux-gnu-cc supports -fno-rtti -fno-exceptions... no
checking for x86_64-conda-linux-gnu-cc option to produce PIC... -fPIC -DPIC
checking if x86_64-conda-linux-gnu-cc PIC flag -fPIC -DPIC works... yes
checking if x86_64-conda-linux-gnu-cc static flag -static works... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... (cached) yes
checking whether the x86_64-conda-linux-gnu-cc linker (/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... x86_64-conda-linux-gnu-c++ -std=gnu++17 -E
checking for ld used by x86_64-conda-linux-gnu-c++ -std=gnu++17... /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-conda-linux-gnu-c++ -std=gnu++17 linker (/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-conda-linux-gnu-c++ -std=gnu++17 option to produce PIC... -fPIC -DPIC
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 static flag -static works... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 supports -c -o file.o... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++17 supports -c -o file.o... (cached) yes
checking whether the x86_64-conda-linux-gnu-c++ -std=gnu++17 linker (/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if we should install only statically linked executables... no
checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking for ceil in -lm... yes
checking for dlopen in -ldl... (cached) yes
checking for egrep... (cached) /usr/bin/grep -E
checking for sys/resource.h... yes
checking for sys/time.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking for sys/file.h... yes
checking for stddef.h... yes
checking for setjmp.h... yes
checking for features.h... yes
checking for dirent.h... yes
checking for stdint.h... (cached) yes
checking for stdbool.h... yes
checking for netdb.h... yes
checking for netinet/in.h... yes
checking for arpa/inet.h... yes
checking for io.h... no
checking for winsock2.h... no
checking for sys/timeb.h... yes
checking for _FILE_OFFSET_BITS value needed for large files... no
checking size of int8_t... 1
checking size of uint8_t... 1
checking size of int_least8_t... 1
checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
checking size of int16_t... 2
checking size of uint16_t... 2
checking size of int_least16_t... 2
checking size of uint_least16_t... 2
checking size of int_fast16_t... 8
checking size of uint_fast16_t... 8
checking size of int32_t... 4
checking size of uint32_t... 4
checking size of int_least32_t... 4
checking size of uint_least32_t... 4
checking size of int_fast32_t... 8
checking size of uint_fast32_t... 8
checking size of int64_t... 8
checking size of uint64_t... 8
checking size of int_least64_t... 8
checking size of uint_least64_t... 8
checking size of int_fast64_t... 8
checking size of uint_fast64_t... 8
checking size of size_t... 8
checking size of ssize_t... 8
checking size of ptrdiff_t... 8
checking size of off_t... 8
checking size of bool... 1
checking size of time_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking for szlib.h... yes
checking for libaec.h... yes
checking for aec_encode in -laec... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... no
checking for thread safe support... no
checking for x86_64-conda-linux-gnu-cc options needed to detect all undeclared functions... none needed
checking whether CLOCK_MONOTONIC is declared... yes
checking for tm_gmtoff in struct tm... yes
checking for global timezone variable... yes
checking for st_blocks in struct stat... no
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for getpwuid... yes
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for library containing clock_gettime... none required
checking for alarm... yes
checking for clock_gettime... yes
checking for difftime... yes
checking for fcntl... yes
checking for flock... yes
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getrusage... yes
checking for gettimeofday... yes
checking for lstat... yes
checking for rand_r... yes
checking for random... yes
checking for setsysinfo... no
checking for signal... yes
checking for longjmp... yes
checking for setjmp... yes
checking for siglongjmp... yes
checking for sigsetjmp... no
checking for sigprocmask... yes
checking for snprintf... yes
checking for srandom... yes
checking for strdup... yes
checking for symlink... yes
checking for system... yes
checking for strtoll... yes
checking for strtoull... yes
checking for tmpfile... yes
checking for asprintf... yes
checking for vasprintf... yes
checking for vsnprintf... yes
checking for waitpid... yes
checking for roundf... yes
checking for lroundf... yes
checking for llroundf... yes
checking for round... yes
checking for lround... yes
checking for llround... yes
checking for an ANSI C-conforming const... yes
checking if the compiler understands __inline__... yes
checking if the compiler understands __inline... yes
checking if the compiler understands inline... yes
checking for __attribute__ extension... yes
checking for __func__ extension... yes
checking for __FUNCTION__ extension... yes
checking for C99 designated initialization support... yes
checking how to print long long... %ld and %lu
checking enable debugging symbols... no
checking enable asserts... no
checking enable developer warnings... no
checking profiling... no
checking optimization level... high
checking enable file locking... best-effort
checking for internal debug output... none
checking whether function stack tracking is enabled... no
checking for API tracing... no
checking whether a memory checking tool will be used... no
checking whether internal memory allocation sanity checking is used... no
checking for parallel support files... skipped
checking whether O_DIRECT is declared... yes
checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking if the Mirror virtual file driver (VFD) is enabled... no
checking for curl/curl.h... yes
checking for openssl/evp.h... yes
checking for openssl/hmac.h... yes
checking for openssl/sha.h... yes
checking for curl_global_init in -lcurl... yes
checking for EVP_sha256 in -lcrypto... yes
checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes
checking for libhdfs... suppressed
checking for custom examples path definition... ${prefix}/share/hdf5_examples
checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if the machine has window style path name... no
checking if using special algorithm to convert long double to (unsigned) long values... no
checking if using special algorithm to convert (unsigned) long to long double values... no
checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
checking if the system is IBM ppc64le and cannot correctly convert some long double values... no
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v110
checking whether to perform strict file format checks... no
checking for pread... yes
checking for pwrite... yes
checking whether to use pread/pwrite instead of read/write in certain VFDs... yes
checking whether to have library information embedded in the executables... yes
checking if alignment restrictions are strictly enforced... no
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating utils/Makefile
config.status: creating utils/mirror_vfd/Makefile
config.status: creating bin/h5cc
config.status: creating bin/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating hl/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/c++/Makefile
config.status: creating hl/c++/src/Makefile
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.7
Configured on: Thu May 29 10:47:50 EDT 2025
Configured by: ggama1@c484
Host system: x86_64-pc-linux-gnu
Uname information: Linux c484 4.18.0-477.21.1.el8_8.x86_64 #1 SMP Tue Aug 8 21:30:09 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static
Statically Linked Executables:
LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lcrypto -lcurl -lsz -laec -lz -ldl -lm
Archiver: x86_64-conda-linux-gnu-ar
AR_FLAGS: cr
Ranlib: x86_64-conda-linux-gnu-ranlib
Languages:
----------
C: yes
C Compiler: /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -I/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -fdebug-prefix-map=/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45=/usr/local/src/conda-prefix -fpic
H5 C Flags: -std=c99 -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3 -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized
AM C Flags:
Shared C Library: no
Static C Library: yes
Fortran: no
C++: yes
C++ Compiler: /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/bin/x86_64-conda-linux-gnu-c++ -std=gnu++17
C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -fdebug-prefix-map=/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45=/usr/local/src/conda-prefix -fpic
H5 C++ Flags: -Wall -Wconversion -Wctor-dtor-privacy -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3 -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow
AM C++ Flags:
Shared C++ Library: no
Static C++ Library: yes
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Build HDF5 Tests: no
Build HDF5 Tools: no
Threadsafety: no
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(no encoder)
MPE: no
Direct VFD: no
Mirror VFD: no
(Read-Only) S3 VFD: yes
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
make[1]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5'
for d in src . c++ hl; do \
if test $d != .; then \
(cd $d && make lib) || exit 1; \
fi; \
done
make[2]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/src'
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/src'
CC H5.lo
CC H5checksum.lo
CC H5dbg.lo
CC H5system.lo
In file included from H5system.c:33:
H5system.c: In function 'H5_build_extpath':
H5private.h:1470:31: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1470 | #define HDstrncat(X,Y,Z) strncat(X,Y,Z)
| ^~~~~~~
H5system.c:1307:13: note: in expansion of macro 'HDstrncat'
1307 | HDstrncat(full_path, new_name, HDstrlen(new_name));
| ^~~~~~~~~
H5private.h:1467:28: note: length computed here
1467 | #define HDstrlen(S) strlen(S)
| ^~~~~~~~~
H5private.h:1470:43: note: in definition of macro 'HDstrncat'
1470 | #define HDstrncat(X,Y,Z) strncat(X,Y,Z)
| ^
H5system.c:1307:44: note: in expansion of macro 'HDstrlen'
1307 | HDstrncat(full_path, new_name, HDstrlen(new_name));
| ^~~~~~~~
CC H5timer.lo
In file included from /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/stdio.h:937,
from H5private.h:56,
from H5timer.c:32:
In function 'sprintf',
inlined from 'H5_timer_get_time_string' at H5timer.c:658:9:
/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/bits/stdio2.h:33:10: warning: 'hours' may be used uninitialized [-Wmaybe-uninitialized]
33 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5timer.c: In function 'H5_timer_get_time_string':
H5timer.c:601:12: note: 'hours' was declared here
601 | double hours;
| ^~~~~
In function 'sprintf',
inlined from 'H5_timer_get_time_string' at H5timer.c:658:9:
/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/bits/stdio2.h:33:10: warning: 'minutes' may be used uninitialized [-Wmaybe-uninitialized]
33 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5timer.c: In function 'H5_timer_get_time_string':
H5timer.c:602:12: note: 'minutes' was declared here
602 | double minutes;
| ^~~~~~~
In function 'sprintf',
inlined from 'H5_timer_get_time_string' at H5timer.c:658:9:
/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/bits/stdio2.h:33:10: warning: 'remainder_sec' may be used uninitialized [-Wmaybe-uninitialized]
33 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5timer.c: In function 'H5_timer_get_time_string':
H5timer.c:603:12: note: 'remainder_sec' was declared here
603 | double remainder_sec;
| ^~~~~~~~~~~~~
In function 'sprintf',
inlined from 'H5_timer_get_time_string' at H5timer.c:658:9:
/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/bits/stdio2.h:33:10: warning: 'days' may be used uninitialized [-Wmaybe-uninitialized]
33 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5timer.c: In function 'H5_timer_get_time_string':
H5timer.c:600:12: note: 'days' was declared here
600 | double days;
| ^~~~
CC H5trace.lo
CC H5A.lo
CC H5Abtree2.lo
CC H5Adense.lo
H5Adense.c: In function 'H5A__dense_fnd_cb':
H5Adense.c:314:27: warning: initialization discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
314 | H5A_t *old_attr = *user_attr;
| ^
CC H5Adeprec.lo
CC H5Aint.lo
CC H5Atest.lo
CC H5AC.lo
CC H5ACdbg.lo
CC H5ACproxy_entry.lo
CC H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2internal.lo
CC H5B2leaf.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5Cdbg.lo
CC H5Cepoch.lo
CC H5Cimage.lo
In file included from H5Cprivate.h:35,
from H5Cpkg.h:37,
from H5Cimage.c:42:
H5Cimage.c: In function 'H5C__reconstruct_cache_entry':
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Cimage.c:3397:5: note: in expansion of macro 'INT32DECODE'
3397 | INT32DECODE(p, pf_entry_ptr->lru_rank);
| ^~~~~~~~~~~
CC H5Clog.lo
CC H5Clog_json.lo
CC H5Clog_trace.lo
CC H5Cprefetched.lo
CC H5Cquery.lo
CC H5Ctag.lo
CC H5Ctest.lo
CC H5CS.lo
CC H5CX.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dbtree2.lo
CC H5Dchunk.lo
H5Dchunk.c: In function 'H5D__create_chunk_file_map_hyper':
H5Dchunk.c:1873:40: warning: passing argument 1 of 'H5S_combine_hyperslab' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
1873 | if(H5S_combine_hyperslab(fm->file_space, H5S_SELECT_AND, coords, NULL, fm->chunk_dim, NULL, &tmp_fchunk) < 0)
| ~~^~~~~~~~~~~~
In file included from H5Rprivate.h:26,
from H5Tprivate.h:32,
from H5Zprivate.h:28,
from H5CXprivate.h:30,
from H5Dchunk.c:55:
H5Sprivate.h:313:44: note: expected 'H5S_t *' but argument is of type 'const H5S_t *'
313 | H5_DLL herr_t H5S_combine_hyperslab(H5S_t *old_space, H5S_seloper_t op,
| ~~~~~~~^~~~~~~~~
H5Dchunk.c: In function 'H5D__chunk_allocate':
H5Dchunk.c:4433:32: warning: cast between incompatible function types from 'void * (*)(void *, const H5O_pline_t *)' to 'void (*)(void *, void *)' [-Wcast-function-type]
4433 | (void *)pline, (H5MM_free_t)H5D__chunk_mem_xfree, (void *)pline,
| ^
H5Dchunk.c:4482:22: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
4482 | idx_info.storage = sc;
| ^
H5Dchunk.c: In function 'H5D__chunk_copy_cb':
H5Dchunk.c:6159:111: warning: passing argument 5 of 'H5D__chunk_file_alloc' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
6159 | _dst, NULL, &udata_dst.chunk_block, &need_insert, udata_dst.common.scaled) < 0)
| ~~~~~~~~~~~~~~~~^~~~~~~
In file included from H5Dchunk.c:56:
H5Dpkg.h:653:59: note: expected 'hsize_t *' {aka 'long long unsigned int *'} but argument is of type 'const hsize_t *' {aka 'const long long unsigned int *'}
653 | H5F_block_t *new_chunk, hbool_t *need_insert, hsize_t scaled[]);
| ~~~~~~~~^~~~~~~~
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Dearray.lo
CC H5Defl.lo
CC H5Dfarray.lo
CC H5Dfill.lo
CC H5Dint.lo
H5Dint.c:100:21: warning: size of 'H5D_def_dset' 4672 bytes exceeds maximum object size 2560 [-Wlarger-than=]
100 | static H5D_shared_t H5D_def_dset;
| ^~~~~~~~~~~~
In file included from H5Dint.c:24:
H5Dint.c: In function 'H5D_nameof':
H5Dint.c:2230:49: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
2230 | FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : NULL)
H5private.h:2437:12: note: in definition of macro 'FUNC_LEAVE_NOAPI'
2437 | return(ret_value); \
| ^~~~~~~~~
H5Dint.c: In function 'H5D_flush_all':
H5Dint.c:3327:52: warning: passing argument 3 of 'H5I_iterate' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
3327 | if(H5I_iterate(H5I_DATASET, H5D__flush_all_cb, f, FALSE) < 0) /* Casting away const OK -QAK */
| ^
In file included from H5Dint.c:31:
H5Iprivate.h:70:74: note: expected 'void *' but argument is of type 'const H5F_t *'
70 | herr_t H5I_iterate(H5I_type_t type, H5I_search_func_t func, void *udata, hbool_t app_ref);
| ~~~~~~^~~~~
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dnone.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dsingle.lo
CC H5Dtest.lo
CC H5Dvirtual.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5EA.lo
CC H5EAcache.lo
CC H5EAdbg.lo
CC H5EAdblkpage.lo
CC H5EAdblock.lo
CC H5EAhdr.lo
CC H5EAiblock.lo
CC H5EAint.lo
CC H5EAsblock.lo
CC H5EAstat.lo
CC H5EAtest.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fcwfs.lo
CC H5Fdbg.lo
CC H5Fdeprec.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fint.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fspace.lo
CC H5Fsuper.lo
H5Fsuper.c: In function 'H5F__super_read':
H5Fsuper.c:528:11: warning: this condition has identical branches [-Wduplicated-branches]
528 | if(H5F_addr_lt(super_addr, sblock->base_addr))
| ^
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FA.lo
CC H5FAcache.lo
CC H5FAdbg.lo
CC H5FAdblock.lo
CC H5FAdblkpage.lo
CC H5FAhdr.lo
CC H5FAint.lo
CC H5FAstat.lo
CC H5FAtest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDfamily.lo
CC H5FDhdfs.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDsplitter.lo
CC H5FDstdio.lo
CC H5FDtest.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSint.lo
CC H5FSsection.lo
CC H5FSstat.lo
CC H5FStest.lo
CC H5G.lo
CC H5Gbtree2.lo
CC H5Gcache.lo
CC H5Gcompact.lo
CC H5Gdense.lo
CC H5Gdeprec.lo
CC H5Gent.lo
CC H5Gint.lo
CC H5Glink.lo
CC H5Gloc.lo
CC H5Gname.lo
CC H5Gnode.lo
CC H5Gobj.lo
CC H5Goh.lo
CC H5Groot.lo
CC H5Gstab.lo
CC H5Gtest.lo
CC H5Gtraverse.lo
CC H5HF.lo
CC H5HFbtree2.lo
CC H5HFcache.lo
H5HFcache.c: In function 'H5HF__cache_hdr_serialize':
H5HFcache.c:770:12: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
770 | hdr->f = f;
| ^
H5HFcache.c: In function 'H5HF__cache_iblock_serialize':
H5HFcache.c:1360:12: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
1360 | hdr->f = f;
| ^
CC H5HFdbg.lo
CC H5HFdblock.lo
CC H5HFdtable.lo
CC H5HFhdr.lo
CC H5HFhuge.lo
H5HFhuge.c: In function 'H5HF__huge_write':
H5HFhuge.c:863:8: warning: 'obj_size' may be used uninitialized [-Wmaybe-uninitialized]
863 | if(H5F_block_write(hdr->f, H5FD_MEM_FHEAP_HUGE_OBJ, obj_addr, obj_size, obj) < 0)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5HFhuge.c:810:12: note: 'obj_size' was declared here
810 | size_t obj_size; /* Object's size in the file */
| ^~~~~~~~
CC H5HFiblock.lo
CC H5HFiter.lo
CC H5HFman.lo
CC H5HFsection.lo
CC H5HFspace.lo
CC H5HFstat.lo
CC H5HFtest.lo
CC H5HFtiny.lo
CC H5HG.lo
CC H5HGcache.lo
CC H5HGdbg.lo
CC H5HGquery.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HLprfx.lo
CC H5HLdblk.lo
CC H5HP.lo
CC H5I.lo
H5I.c: In function 'H5I__id_dump_cb':
H5I.c:2135:31: warning: passing argument 1 of 'H5G_nameof' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
2135 | path = H5G_nameof((const H5G_t *)item->obj_ptr);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from H5Tprivate.h:31,
from H5Zprivate.h:28,
from H5CXprivate.h:30,
from H5I.c:34:
H5Gprivate.h:190:39: note: expected 'H5G_t *' but argument is of type 'const H5G_t *'
190 | H5_DLL H5G_name_t * H5G_nameof(H5G_t *grp);
| ~~~~~~~^~~
H5I.c: At top level:
H5I.c:125:12: warning: 'H5I__debug_cb' declared 'static' but never defined [-Wunused-function]
125 | static int H5I__debug_cb(void *_item, void *_key, void *_udata);
| ^~~~~~~~~~~~~
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5make_libsettings > H5lib_settings.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
H5lib_settings.c:31:6: warning: size of 'H5libhdf5_settings' 6760 bytes exceeds maximum object size 2560 [-Wlarger-than=]
31 | char H5libhdf5_settings[]=
| ^~~~~~~~~~~~~~~~~~
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Odeprec.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ocache_image.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
In file included from H5Cprivate.h:35,
from H5ACprivate.h:33,
from H5Oprivate.h:41,
from H5Dprivate.h:25,
from H5Ofill.c:25:
H5Ofill.c: In function 'H5O_fill_new_decode':
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Ofill.c:228:13: note: in expansion of macro 'INT32DECODE'
228 | INT32DECODE(p, fill->size);
| ^~~~~~~~~~~
CC H5Oflush.lo
CC H5Ofsinfo.lo
H5Ofsinfo.c: In function 'H5O_fsinfo_decode':
H5Ofsinfo.c:130:35: warning: 'threshold' may be used uninitialized [-Wmaybe-uninitialized]
130 | fsinfo->threshold = threshold;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
H5Ofsinfo.c:112:17: note: 'threshold' was declared here
112 | hsize_t threshold; /* Threshold */
| ^~~~~~~~~
CC H5Oginfo.lo
CC H5Oint.lo
CC H5Olayout.lo
H5Olayout.c: In function 'H5O__layout_decode':
H5Olayout.c:417:120: warning: 'tmp_hsize' may be used uninitialized [-Wmaybe-uninitialized]
417 | list = (H5O_storage_virtual_ent_t *)H5MM_calloc((size_t)tmp_hsize * sizeof(H5O_storage_virtual_ent_t))))
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5Olayout.c:397:29: note: 'tmp_hsize' was declared here
397 | hsize_t tmp_hsize;
| ^~~~~~~~~
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Oshmesg.lo
CC H5Ostab.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pencdec.lo
CC H5Pfapl.lo
In file included from H5Cprivate.h:35,
from H5ACprivate.h:33,
from H5Pfapl.c:34:
H5Pfapl.c: In function 'H5P__facc_cache_image_config_dec':
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pfapl.c:3073:5: note: in expansion of macro 'INT32DECODE'
3073 | INT32DECODE(*pp, config->version);
| ^~~~~~~~~~~
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pfapl.c:3079:5: note: in expansion of macro 'INT32DECODE'
3079 | INT32DECODE(*pp, config->entry_ageout);
| ^~~~~~~~~~~
H5Pfapl.c: In function 'H5P__facc_cache_config_dec':
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pfapl.c:3603:5: note: in expansion of macro 'INT32DECODE'
3603 | INT32DECODE(*pp, config->version);
| ^~~~~~~~~~~
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pfapl.c:3677:5: note: in expansion of macro 'INT32DECODE'
3677 | INT32DECODE(*pp, config->epochs_before_eviction);
| ^~~~~~~~~~~
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pfapl.c:3687:5: note: in expansion of macro 'INT32DECODE'
3687 | INT32DECODE(*pp, config->metadata_write_strategy);
| ^~~~~~~~~~~
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
In file included from H5Cprivate.h:35,
from H5ACprivate.h:33,
from H5Oprivate.h:41,
from H5Opkg.h:22,
from H5Pocpl.c:40:
H5Pocpl.c: In function 'H5P__ocrt_pipeline_dec':
H5Fprivate.h:168:71: warning: this condition has identical branches [-Wduplicated-branches]
168 | ((*(p) & (unsigned)0x80) ? (unsigned)(~0xffffffff) : (unsigned)0x0))); (p)++; \
| ^
H5Pocpl.c:1517:9: note: in expansion of macro 'INT32DECODE'
1517 | INT32DECODE(*pp, filter.id)
| ^~~~~~~~~~~
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5PB.lo
CC H5PL.lo
CC H5PLint.lo
CC H5PLpath.lo
CC H5PLplugin_cache.lo
CC H5R.lo
CC H5Rint.lo
CC H5Rdeprec.lo
CC H5UC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
H5Shyper.c:3531:1: warning: 'H5S__hyper_get_enc_size_real' defined but not used [-Wunused-function]
3531 | H5S__hyper_get_enc_size_real(hsize_t max_size)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
In file included from H5SL.c:64:
H5SL.c: In function 'H5SL_insert_common':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
2437 | return(ret_value); \
| ^
H5SL.c:846:5: note: in expansion of macro 'FUNC_LEAVE_NOAPI'
846 | FUNC_LEAVE_NOAPI(ret_value)
| ^~~~~~~~~~~~~~~~
H5SL.c:760:18: note: 'ret_value' was declared here
760 | H5SL_node_t *ret_value; /* Return value */
| ^~~~~~~~~
H5SL.c: In function 'H5SL_search':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
2437 | return(ret_value); \
| ^
H5SL.c:1459:5: note: in expansion of macro 'FUNC_LEAVE_NOAPI'
1459 | FUNC_LEAVE_NOAPI(ret_value)
| ^~~~~~~~~~~~~~~~
H5SL.c:1397:11: note: 'ret_value' was declared here
1397 | void *ret_value; /* Return value */
| ^~~~~~~~~
H5SL.c: In function 'H5SL_find':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
2437 | return(ret_value); \
| ^
H5SL.c:1760:5: note: in expansion of macro 'FUNC_LEAVE_NOAPI'
1760 | FUNC_LEAVE_NOAPI(ret_value)
| ^~~~~~~~~~~~~~~~
H5SL.c:1698:18: note: 'ret_value' was declared here
1698 | H5SL_node_t *ret_value; /* Return value */
| ^~~~~~~~~
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
H5T.c: In function 'H5T_nameof':
H5T.c:5246:23: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
5246 | ret_value = &(dt->path);
| ^
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5Tinit.c ; exit 1)
CC H5Tinit.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5VM.lo
CC H5WB.lo
CC H5Z.lo
CC H5Zdeflate.lo
CC H5Zfletcher32.lo
CC H5Znbit.lo
CC H5Zshuffle.lo
CC H5Zscaleoffset.lo
CC H5Zszip.lo
CC H5Ztrans.lo
CC H5FDros3.lo
CC H5FDs3comms.lo
In file included from /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/string.h:638,
from H5private.h:58,
from H5FDs3comms.c:41:
In function 'strncpy',
inlined from 'H5FD_s3comms_parse_url' at H5FDs3comms.c:2308:5:
/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string3.h:120:10: warning: '__builtin_strncpy' specified size between 9223372036854775808 and 0 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
120 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CCLD libhdf5.la
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/src'
make[2]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++'
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++'
make[3]: Nothing to be done for 'build-lib'.
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++'
+ cd src
+ make lib
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++/src'
make[4]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++/src'
CXX H5Exception.lo
CXX H5IdComponent.lo
CXX H5DataSpace.lo
CXX H5PropList.lo
CXX H5Library.lo
CXX H5FaccProp.lo
CXX H5FcreatProp.lo
CXX H5LcreatProp.lo
CXX H5LaccProp.lo
CXX H5DaccProp.lo
CXX H5DxferProp.lo
CXX H5DcreatProp.lo
CXX H5Location.lo
CXX H5AbstractDs.lo
CXX H5Attribute.lo
CXX H5Object.lo
H5Object.cpp:45:19: warning: no previous declaration for 'herr_t H5::userAttrOpWrpr(hid_t, const char*, const H5A_info_t*, void*)' [-Wmissing-declarations]
45 | extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
| ^~~~~~~~~~~~~~
H5Object.cpp: In function 'herr_t H5::userAttrOpWrpr(hid_t, const char*, const H5A_info_t*, void*)':
H5Object.cpp:45:40: warning: unused parameter 'loc_id' [-Wunused-parameter]
45 | extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
| ~~~~~~^~~~~~
H5Object.cpp:46:23: warning: unused parameter 'ainfo' [-Wunused-parameter]
46 | const H5A_info_t *ainfo, void *op_data)
| ~~~~~~~~~~~~~~~~~~^~~~~
H5Object.cpp: At global scope:
H5Object.cpp:56:19: warning: no previous declaration for 'herr_t H5::userVisitOpWrpr(hid_t, const char*, const H5O_info_t*, void*)' [-Wmissing-declarations]
56 | extern "C" herr_t userVisitOpWrpr(hid_t obj_id, const char *attr_name,
| ^~~~~~~~~~~~~~~
H5Object.cpp: In function 'herr_t H5::userVisitOpWrpr(hid_t, const char*, const H5O_info_t*, void*)':
H5Object.cpp:56:41: warning: unused parameter 'obj_id' [-Wunused-parameter]
56 | extern "C" herr_t userVisitOpWrpr(hid_t obj_id, const char *attr_name,
| ~~~~~~^~~~~~
CXX H5OcreatProp.lo
CXX H5DataType.lo
CXX H5AtomType.lo
CXX H5PredType.lo
H5PredType.cpp: In member function 'void H5::PredType::commit(H5::H5Location&, const char*)':
H5PredType.cpp:86:35: warning: unused parameter 'loc' [-Wunused-parameter]
86 | void PredType::commit(H5Location& loc, const char* name)
| ~~~~~~~~~~~~^~~
H5PredType.cpp:86:52: warning: unused parameter 'name' [-Wunused-parameter]
86 | void PredType::commit(H5Location& loc, const char* name)
| ~~~~~~~~~~~~^~~~
CXX H5EnumType.lo
CXX H5IntType.lo
CXX H5FloatType.lo
CXX H5StrType.lo
H5StrType.cpp: In constructor 'H5::StrType::StrType(int, const size_t&)':
H5StrType.cpp:105:28: warning: unused parameter 'dummy' [-Wunused-parameter]
105 | StrType::StrType(const int dummy, const size_t& size) : AtomType()
| ~~~~~~~~~~^~~~~
CXX H5ArrayType.lo
CXX H5VarLenType.lo
CXX H5CompType.lo
CXX H5DataSet.lo
CXX H5CommonFG.lo
CXX H5Group.lo
CXX H5File.lo
CXXLD libhdf5_cpp.la
make[4]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++/src'
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++/src'
make[2]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl'
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl'
make[3]: Nothing to be done for 'build-lib'.
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl'
+ cd src
+ make lib
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/src'
make[4]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/src'
CC H5DO.lo
CC H5DS.lo
CC H5IM.lo
CC H5LT.lo
CC H5LTanalyze.lo
CC H5LTparse.lo
CC H5PT.lo
CC H5TB.lo
CC H5LD.lo
CCLD libhdf5_hl.la
make[4]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/src'
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/src'
+ cd c++
+ make lib
make[3]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++'
make[4]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++'
make[4]: Nothing to be done for 'build-lib'.
make[4]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++'
+ cd src
+ make lib
make[4]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++/src'
make[5]: Entering directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++/src'
CXX H5PacketTable.lo
CXXLD libhdf5_hl_cpp.la
make[5]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++/src'
make[4]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++/src'
make[3]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl/c++'
make[2]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5/hl'
make[1]: Leaving directory '/tmp/RtmpLo5ulI/R.INSTALL3eaf038ce5ae4/Rhdf5lib/src/hdf5'
mkdir -p "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/*.h "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src"/*.h "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src"/*.h "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src"/*.h "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/libhdf5.settings "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
x86_64-conda-linux-gnu-cc -I"/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/include" -DNDEBUG -I"/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -I/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -fdebug-prefix-map=/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45=/usr/local/src/conda-prefix -c Rhdf5lib.c -o Rhdf5lib.o
x86_64-conda-linux-gnu-cc -shared -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -Wl,-rpath-link,/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib -o Rhdf5lib.so Rhdf5lib.o /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a -lsz -laec -lz -L/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/lib -lR
installing to /scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Rhdf5lib’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/Rhdf5lib.so':
libsz.so.2: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/scratch4/nsobrei2/ggama1/conda/.conda/envs/r45/lib/R/library/Rhdf5lib’
The downloaded source packages are in
‘/tmp/RtmpQBZexe/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘Rhdf5lib’ had non-zero exit status