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pCMF example gives segmentation fault #1
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Thank you very much for this report, I am quite busy at the moment, I will try to find the problem later in the day. Thanks again |
@gdurif Thank you. Please let me know if you cannot reproduce the error. |
I am not able to reproduce the bug (I don't have MacOS to run some tests). Do you know which compiler is used when R install the package and which version of pCMF did you install? (prod or prod_no_omp?) |
@gdurif I re-installed |
Ok, I guess the problem is with the compiler. On MacOS, OpenMP support in the compiler can be an issue. I will try to find the problem anyway. |
@gdurif I'm not using the compiler provided by Apple. I'm using a version of clang installed via MacPorts: CC = /opt/local/bin/clang-mp-4.0
CXX = /opt/local/bin/clang++-mp-4.0
CXX11 = /opt/local/bin/clang++-mp-4.0
CXX17 = /opt/local/bin/clang++-mp-4.0
CXX98 = /opt/local/bin/clang++-mp-4.0
CXX1X = /opt/local/bin/clang++-mp-4.0
F77 = /opt/local/bin/gfortran-mp-6
FC = /opt/local/bin/gfortran-mp-6
LDFLAGS = -L/opt/local/lib # -L/usr/local/Cellar/hdf5/1.10.1_2/lib
FLIBS = -L/opt/local/lib/gcc6 -lgfortran -lquadmath -lm See here for details. |
Thanks for this information. |
Hi, I don't think that a MacOS problem. Your example run smoothly on : > sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin18.6.0 (64-bit)
Running under: macOS Catalina 10.15.1
Matrix products: default
BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.7/lib/libopenblasp-r0.3.7.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pCMF_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 pillar_1.4.2 compiler_3.6.1
[4] prettyunits_1.0.2 remotes_2.1.0 tools_3.6.1
[7] testthat_2.3.0 digest_0.6.22 pkgbuild_1.0.6
[10] dotCall64_1.0-0 pkgload_1.0.2 tibble_2.1.3
[13] memoise_1.1.0 lifecycle_0.1.0 gtable_0.3.0
[16] lattice_0.20-38 pkgconfig_2.0.3 rlang_0.4.1
[19] Matrix_1.2-17 cli_1.1.0 curl_3.3
[22] spam_2.4-0 dplyr_0.8.3 withr_2.1.2
[25] desc_1.2.0 fs_1.3.1 fields_10.0
[28] devtools_2.1.0 maps_3.3.0 tidyselect_0.2.5
[31] rprojroot_1.3-2 grid_3.6.1 glue_1.3.1
[34] R6_2.4.1 processx_3.4.1 sessioninfo_1.1.1
[37] purrr_0.3.2 callr_3.3.2 ggplot2_3.2.1
[40] magrittr_1.5 backports_1.1.5 scales_1.1.0
[43] ps_1.3.0 usethis_1.5.1 assertthat_0.2.1
[46] colorspace_1.4-1 lazyeval_0.2.2 munsell_0.5.0
[49] crayon_1.3.4 RcppEigen_0.3.3.7.0 my
|
@l-modolo Thanks for that info. Your compiler setup isn't the one recommended by CRAN (you should be using clang), but glad to know that it can work on macOS. |
Hi @gdurif, I tried to use your R package. I was able to successfully install the package, but I ran into trouble when trying to run the cNMF example provided. This is the error I get:
This is the exact code I ran (note that I added a
set.seed
; without it, your example is not reproducible):Please advise. Note that I am using R 3.4.3 on a MacBook Pro:
The text was updated successfully, but these errors were encountered: