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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

ANTsRCore build failing #337

Closed muratmaga closed 3 years ago

muratmaga commented 3 years ago

Our sysadmins recently migrated to R 4.0.3 and the toolchain to gcc 10 on the cluster (based on centos 7.8).

I am getting this error building ANTsX from scratch. I am using the install_github method. Cmake is 3.19.0. ITKR installs fine. Is there any known issues with gcc 10, or any suggestions about where the issue might be coming from?

Describe the bug ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘ANTsRCore’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/gpfs/home/amaga/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-ANTsRCore/00new/ANTsRCore/libs/ANTsRCore.so': /gpfs/home/amaga/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-ANTsRCore/00new/ANTsRCore/libs/ANTsRCore.so: undefined symbol: _ZN4ants16antsRegistrationESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS6_EEPSo

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /gpfs/nfs-depot/apps/R/4.0.3_gcc-10.2.0/lib64/R/lib/libRblas.so LAPACK: /gpfs/nfs-depot/apps/R/4.0.3_gcc-10.2.0/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] devtools_2.3.2 usethis_2.0.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.5 compiler_4.0.3 prettyunits_1.1.1 base64enc_0.1-3
[5] remotes_2.2.0 tools_4.0.3 testthat_3.0.0 digest_0.6.27
[9] pkgbuild_1.2.0 pkgload_1.1.0 jsonlite_1.7.2 memoise_1.1.0
[13] lifecycle_0.2.0 lattice_0.20-41 rlang_0.4.9 Matrix_1.2-18
[17] cli_2.2.0 rstudioapi_0.13 curl_4.3 withr_2.3.0
[21] desc_1.2.0 fs_1.5.0 rappdirs_0.3.1 rprojroot_2.0.2
[25] grid_4.0.3 reticulate_1.18 glue_1.4.2 R6_2.5.0
[29] processx_3.4.5 fansi_0.4.1 sessioninfo_1.1.1 purrr_0.3.4
[33] callr_3.5.1 magrittr_2.0.1 whisker_0.4 ps_1.5.0
[37] tfruns_1.4 ellipsis_0.3.1 assertthat_0.2.1 tensorflow_2.2.0 [41] crayon_1.3.4

.libPaths() [1] "/gpfs/home/amaga/R/x86_64-pc-linux-gnu-library/4.0"
[2] "/gpfs/nfs-depot/apps/R/4.0.3_gcc-10.2.0/lib64/R/library"

muratmaga commented 3 years ago

I am not sure what the issue was, but reverting to gcc 7.3.0-20 tool chain fixed the issue.