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rnakato / ShortCake

A docker image for single-cell analysis
https://hub.docker.com/r/rnakato/shortcake
GNU General Public License v3.0
66 stars 13 forks source link

Error running R #1

Closed mspivakov closed 1 year ago

mspivakov commented 2 years ago

Hello! I find your container really helpful, as a few of these packages are a real pain to install. The singularity container has installed without errors, however, when I try to execute it, I get:

$ singularity exec rnakato_singlecell_jupyter.img R ERROR: ld.so: object '/apps/rcs-setxattr-replacement/rcs-setxattr-replacement/libc-setxattr-shim.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpnam.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpfile.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-setxattr-replacement/rcs-setxattr-replacement/libc-setxattr-shim.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpnam.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpfile.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-setxattr-replacement/rcs-setxattr-replacement/libc-setxattr-shim.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpnam.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/apps/rcs-tmpfile-replacement/rcs-tmpfile-replacement/libc-replaced-tmpfile.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. Fatal error: 'R_TempDir' を作成することができません

My understanding is that I have some permissions issue with R_TempDir. Do you have any suggestions on how this could be fixed? Many thanks!

rnakato commented 2 years ago

I am sorry I didn't notice your question. Do you use the LD_PRELOAD variable in your environment? Or, did you try to install the R package in the singularity image?