Open fizwit opened 4 months ago
Could you please show me sessionInfo()
?
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.11.0
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
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.3
I am experiencing a similar problem on R-4.3.2 and GCC:
g++ -std=gnu++17 <...> -fpic -O2 -ftree-vectorize -march=cascadelake -fno-math-errno -c vectorization.cpp -o vectorization.o
vectorization.cpp: In function ‘const char* vec_char_find_CRLF(const char*, size_t)’:
vectorization.cpp:1878:1: error: jump to label ‘tail’
1878 | tail:
| ^~~~
vectorization.cpp:1849:9: note: from here
1849 | goto tail;
| ^~~~
vectorization.cpp:1855:16: note: crosses initialization of ‘const __m256i mask4’
1855 | const __m256i mask4 = _mm256_set1_epi8('\r');
| ^~~~~
vectorization.cpp:1854:16: note: crosses initialization of ‘const __m256i mask3’
1854 | const __m256i mask3 = _mm256_set1_epi8('\n');
| ^~~~~
make: *** [<...>/R/4.3.2-foss-2020a/lib64/R/etc/Makeconf:200: vectorization.o] Error 1
ERROR: compilation failed for package ‘SeqArray’
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
Matrix products: default
BLAS/LAPACK: <...>/OpenBLAS/0.3.9-GCC-9.3.0/lib/libopenblas_skylakexp-r0.3.9.so; LAPACK version 3.9.0
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
time zone: Europe/Amsterdam
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.2 BiocManager_1.30.22
The latest commit should fix this issue: https://github.com/zhengxwen/SeqArray/commit/16bba1eba7e4935f13c72026974e9c12720aa23a
Install SeqArray_1.44.0 from Bioconductor or install from GitHub.
Best,
Xiuwen