Compiling error in R-4.3 #20
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I am suffering from the exact same error with the R 4.3 environment. Any solutions? |
Are you also using R and/or compilers installed with conda? Can you include the full output from the package installation here? |
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Also having this issue. Trying to rebuild an {renv} environment that I developed on my laptop. I tried installing the bioconda package Conda environment: Install error output below: |
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Hi @grimbough I am using conda environment, and used BiocManager::install("rhdf5filters"). Also tried to install by conda install -c bioconda bioconductor-rhdf5filters but it takes forever. Here is my error make[2]: *** [Makefile:9: v0/vbz_streamvbyte.o] Error 1
make[2]: Leaving directory '/tmp/RtmpTRrny6/R.INSTALL1fc432d2d0eed/rhdf5filters/src/vbz/vbz'
make[1]: *** [Makefile:25: vbz] Error 2
make[1]: Leaving directory '/tmp/RtmpTRrny6/R.INSTALL1fc432d2d0eed/rhdf5filters/src/vbz'
make: *** [Makevars:29: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/home/rchung/miniconda3/envs/r_env/lib/R/library/rhdf5filters’
* restoring previous ‘/home/rchung/miniconda3/envs/r_env/lib/R/library/rhdf5filters’
The downloaded source packages are in
‘/tmp/Rtmpk2gYJ5/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done |
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Thank you everyone for the extra information. Could you try running this command to install a version that hopefully fixes the issue: BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda") |
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Hi @grimbough , for me still, the same error occurs Thank you! |
This succeeds for me, but package version installed is |
Hello @grimbough, |
Thanks. It be great if you could include a copy of the output so I can try and figure out what compiler settings are wrong. Everything after |
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Thanks for the quick reply. Here it is: |
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Thanks @dlsoltero This seems a bit strange, as it looks the changes I made aren't being reflected in your installation. I would now expect the second line in the output you included to end with: where the important part is If possible, could you try installing again, and somewhere near the start of the output there will be a line saying configure: configuring the VBZ filter
Using rhdf5filters sse3-conda branch
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
Setting VBZ and STREAMBYTE flags
Substituting real VBZ and STREAMBYTE flags
configure: finished configuring the VBZ filterFor easy reference, the install command is: BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda") |
Thanks for the help @grimbough, I'm not sure what was the problem but I did a clean install of the whole conda environment and that fixed the issue. |
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Hi, I have this error while compiling rhdf5filters on R 4.3. Any hint?
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