Error with Rhtslib
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anand_mt ▴ 80
@anand_mt-10016
Last seen 6 days ago

I am trying to read a BAM file using Rhtslib so that I can use the output for downstream analysis. But when I compile the C code and run it in R, the session abruptly crashes.

Here is a sample code:

temp.c

#include "htslib/sam.h"
#include <stdio.h>
#include <stdlib.h>

int parse_bam(const char *bam){

  samFile *fp_in = hts_open(bam,"r");
  sam_close(fp_in);

  printf("Yay!\n");

  return 0;
}

Compiles successfully.

 R CMD SHLIB temp.c 

#gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-#protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c temp.c -o temp.o
#gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o temp.so temp.o /home/anand/R/x86_64-pc-linux-gnu-#library/4.0/Rhtslib/usrlib/libhts.a -lcurl -L/usr/lib/R/lib -lR

When I import the so and run it inside R, it crashes. The test.bam file exists btw.

> dyn.load("temp.so")
> .C("parse_bam", as.character("../test.bam"))
[E::hts_open_format] Failed to open file �±�eU

 *** caught segfault ***
address 0x44, cause 'memory not mapped'

Traceback:
 1: .C("parse_bam", as.character("../test.bam"))

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

I cant seem to figure out the issue. Could anyone please suggest me how to debug it?

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 18.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2    tinytex_0.30   xfun_0.21

P.S: The same C code works perfectly when compiled and run from the terminal.

Rhts Rhtslib • 52 views
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