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grimbough / rhdf5filters

Distributing additional HDF5 compression filters as an R package. Intended to be used with rhdf5, however the compiled filters can also be used with external applications.
https://bioconductor.org/packages/rhdf5filters/
BSD 2-Clause "Simplified" License
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Compilation errors #10

Closed b524198065 closed 3 years ago

b524198065 commented 3 years ago

Hi, when I used R 4.0.3 to install this package, some errors occurred:

Could you please help me indicate what happened and how can I resolve it? Thanks!

x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /vol1/agis/huangsanwen_group/lihongbo/software/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1611775910217/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/vol1/agis/huangsanwen_group/lihongbo/software/miniconda3=/usr/local/src/conda-prefix -fpic -I. -I./common -DXXHNAMESPACE=ZSTD -c compress/zstd_compress.c -o compress/zstd_compress.o compress/zstd_compress.c: In function 'ZSTD_CCtx_setParameter': compress/zstd_compress.c:434:16: warning: implicit declaration of function 'ZSTD_CCtxParam_setParameter'; did you mean 'ZSTD_CCtxParams_setParameter'? [-Wimplicit-function-declaration] 434 | return ZSTD_CCtxParam_setParameter(&cctx->requestedParams, param, value); | ^~~~~~~ | ZSTD_CCtxParams_setParameter compress/zstd_compress.c: At top level: compress/zstd_compress.c:486:8: error: conflicting types for 'ZSTD_CCtxParam_setParameter' 486 | size_t ZSTD_CCtxParam_setParameter(ZSTD_CCtx_params* CCtxParams, | ^~~~~~~ compress/zstd_compress.c:434:16: note: previous implicit declaration of 'ZSTD_CCtxParam_setParameter' was here 434 | return ZSTD_CCtxParam_setParameter(&cctx->requestedParams, param, value); | ^~~~~~~ compress/zstd_compress.c: In function 'ZSTD_CCtx_getParameter': compress/zstd_compress.c:639:12: warning: implicit declaration of function 'ZSTD_CCtxParam_getParameter'; did you mean 'ZSTD_CCtxParam_setParameter'? [-Wimplicit-function-declaration] 639 | return ZSTD_CCtxParam_getParameter(&cctx->requestedParams, param, value); | ^~~~~~~ | ZSTD_CCtxParam_setParameter compress/zstd_compress.c: At top level: compress/zstd_compress.c:642:8: error: conflicting types for 'ZSTD_CCtxParam_getParameter' 642 | size_t ZSTD_CCtxParam_getParameter( | ^~~~~~~ compress/zstd_compress.c:639:12: note: previous implicit declaration of 'ZSTD_CCtxParam_getParameter' was here 639 | return ZSTD_CCtxParam_getParameter(&cctx->requestedParams, param, value); | ^~~~~~~ make[2]: [Makefile:47: compress/zstd_compress.o] Error 1 make[2]: Leaving directory '/tmp/RtmpfDxQTR/R.INSTALL693e5f939980/rhdf5filters/src/blosc/lib/zstd-1.3.8' make[1]: [Makefile:54: lib/zstd-1.3.8] Error 2 make[1]: Leaving directory '/tmp/RtmpfDxQTR/R.INSTALL693e5f939980/rhdf5filters/src/blosc' make: *** [Makevars:28: blosc/libH5Zblosc.so] Error 2 ERROR: compilation failed for package ‘rhdf5filters’

grimbough commented 3 years ago

Can you provide the command you're running to do the installation?

If you're using a version of R installed with conda, it's normally recommended to also install the packages with conda. You can find the command for installing rhdf5filters in https://anaconda.org/bioconda/bioconductor-rhdf5filters

grimbough commented 3 years ago

Closing due to lack of additional information. Please re-open if this is still an issue.