Issue with hlaAttrBagClass
Closed this issue · 10 comments
Dear Xiuwen Zheng
I yesterday installed the HIBAG package. Unfortunately I am stuck with the example which you provide on the webpage. In particular my R session gets stuck once dealing with hlaAttrBagClass.
Some info on my R session.
It would be great to have your help!
Thanks a lot,
Nicolas
I tried the example in the vignette once more but it failed without any informative error message. Your help would very much appreciated. Thank you, Nicoals
What is sessionInfo()?
Hi @zhengxwen, I am having the same issue when loading the pretrained European model. C stack usage is too lose to the limit.
sessionInfo:
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] HIBAG_1.33.2 data.table_1.14.2 ggplot2_3.3.6 stringr_1.4.1 dplyr_1.0.10
[6] NMF_0.24.0 Biobase_2.56.0 cluster_2.1.3 rngtools_1.5.2 pkgmaker_0.32.2
[11] registry_0.5-1 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.0 S4Vectors_0.34.0
[16] BiocGenerics_0.42.0 maftools_2.12.05
loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.62.0 fs_1.5.2 barplot3d_1.0.1
[5] doParallel_1.0.17 RColorBrewer_1.1-3 tools_4.2.0 utf8_1.2.2
[9] R6_2.5.1 DBI_1.1.3 colorspace_2.0-3 DNAcopy_1.70.0
[13] withr_2.5.0 tidyselect_1.1.2 compiler_4.2.0 cli_3.3.0
[17] DelayedArray_0.22.0 rtracklayer_1.56.1 scales_1.2.1 digest_0.6.29
[21] Rsamtools_2.12.0 XVector_0.36.0 pkgconfig_2.0.3 MatrixGenerics_1.8.1
[25] rlang_1.0.6 rstudioapi_0.14 BiocIO_1.6.0 generics_0.1.3
[29] BiocParallel_1.30.3 RCurl_1.98-1.8 magrittr_2.0.3 GenomeInfoDbData_1.2.8
[33] Matrix_1.5-0 Rcpp_1.0.9 munsell_0.5.0 fansi_1.0.3
[37] lifecycle_1.0.3 stringi_1.7.8 yaml_2.3.5 SummarizedExperiment_1.26.1
[41] zlibbioc_1.42.0 plyr_1.8.7 grid_4.2.0 parallel_4.2.0
[45] crayon_1.5.1 lattice_0.20-45 Biostrings_2.64.0 splines_4.2.0
[49] pillar_1.8.1 comorbidity_1.0.5 rjson_0.2.21 reshape2_1.4.4
[53] codetools_0.2-18 XML_3.99-0.10 glue_1.6.2 RcppParallel_5.1.5
[57] vctrs_0.4.1 foreach_1.5.2 gtable_0.3.1 purrr_0.3.4
[61] assertthat_0.2.1 gridBase_0.4-7 xtable_1.8-4 restfulr_0.0.15
[65] survival_3.3-1 tibble_3.1.8 iterators_1.0.14 GenomicAlignments_1.32.1
gcc versoin:
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.1' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.1)
Also, I noticed that HIBAG might be assuming I have a 32-bit architecture:
> HIBAG::hlaSetKernelTarget("max")
[1] "32-bit, AVX2"
[2] "10.3.0, GNUG_v10.3.0"
[3] "Algorithm SIMD: SSE2 SSE4.2 AVX AVX2 AVX512F AVX512BW AVX512VPOPCNTDQ"
Even though I know R is running on 64-bit:
> .Machine$sizeof.pointer
[1] 8
Would appreciate your looking into this!
Non-windows version should work well.
I guess you are using RStudio.
When I run the script from R console or the command line, I don't see the error of C stack.
But I ran the script in RStudio, this error showed up.
It seems that RStudio triggered this error after hlaModelFromObj(), but model.A is still assigned.
Fix this issue in 1678a9b
or HIBAG_v1.33.3 / HIBAG_v1.34.0 in BioC.
Let me know if the C stack error still occurs.
Thank you @zhengxwen! This commit fixed the issue for me in R studio on Windows. Up to you or the OP to close this issue.
Thanks @zhengxwen ! The commit fixed the issue for me in R studio on Windows.
Hi @zhengxwen, I am having the same issue when loading the pretrained European model. C stack usage is too lose to the limit.
sessionInfo:
R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)Also, I noticed that HIBAG might be assuming I have a 32-bit architecture:
> HIBAG::hlaSetKernelTarget("max") [1] "32-bit, AVX2" [2] "10.3.0, GNUG_v10.3.0" [3] "Algorithm SIMD: SSE2 SSE4.2 AVX AVX2 AVX512F AVX512BW AVX512VPOPCNTDQ"Even though I know R is running on 64-bit:
> .Machine$sizeof.pointer [1] 8Would appreciate your looking into this!
It is fixed in HIBAG_1.34.1 (http://bioconductor.org/packages/HIBAG/).
CHANGES IN VERSION 1.34.1
-------------------------
o fix the compiler warning: sprintf is deprecated
o show "64-bit" correctly when run on Windows