Describe the bug
Compilation fails for ANTsRCore package when building a Docker image on an Macbook Pro with M1 chip. I'm building natively (no emulation) using this Dockerfile. ANTs and ITKR install/compile successfully, however.
#11 3356.7 [output clipped, log limit 1MiB reached]
#11 3369.2 /usr/bin/ld: antsImageMutualInformation.o: in function `Rcpp::SlotProxyPolicy<Rcpp::S4_Impl<Rcpp::PreserveStorage> >::slot(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) [clone .part.273]':
#11 3369.2 /usr/local/lib/R/library/Rcpp/include/Rcpp/exceptions.h:209:(.text+0x14): relocation truncated to fit: R_AARCH64_LD64_GOTPAGE_LO15 against symbol `vtable for Rcpp::not_s4' defined in .data.rel.ro._ZTVN4Rcpp6not_s4E[_ZTVN4Rcpp6not_s4E] section in antsImage.o
#11 3369.2 /usr/bin/ld: /usr/local/lib/R/library/Rcpp/include/Rcpp/exceptions.h:209: warning: too many GOT entries for -fpic, please recompile with -fPIC
#11 3369.2 /usr/bin/ld: final link failed: nonrepresentable section on output
#11 3369.2 collect2: error: ld returned 1 exit status
#11 3369.2 make: *** [/usr/local/lib/R/share/make/shlib.mk:10: ANTsRCore.so] Error 1
#11 3369.3 ERROR: compilation failed for package 'ANTsRCore'
#11 3369.3 * removing '/usr/local/lib/R/library/ANTsRCore'
#11 3370.9 There were 17 warnings (use warnings() to see them)
#11 DONE 3371.1s
Session Info (Container)
sessioninfo::sess
#> - Session info ----------------------------------------------------------------------------------------------------------------------------
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os Debian GNU/Linux 10 (buster)
#> system aarch64, linux-gnu
#> ui X11
#> language (EN)
#> collate C
#> ctype C
#> tz Etc/UTC
#> date 2023-03-02
#> pandoc NA
#>
#> - Packages --------------------------------------------------------------------------------------------------------------------------------
#> package * version date (UTC) lib source
#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.2)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.2)
#>
#> [1] /usr/local/lib/R/library
#>
#> -------------------------------------------------------------------------------------------------------------------------------------------
system.file(package="ITKR")
#> [1] "/usr/local/lib/R/library/ITKR"
Session Info (Local)
session::session_info()
#> ─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os macOS Big Sur ... 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2023-03-02
#> pandoc 2.19.2 @ /usr/local/bin/pandoc
#> ─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
Desktop Container (please complete the following information):
Describe the bug Compilation fails for ANTsRCore package when building a Docker image on an Macbook Pro with M1 chip. I'm building natively (no emulation) using this Dockerfile. ANTs and ITKR install/compile successfully, however.
To Reproduce On an M1 Macbook Pro:
Please include output from
R
docker build
:Session Info (Container)
Session Info (Local)
DesktopContainer (please complete the following information):