Run valgrind on Bioconductor's docker image

docker_valgrind.Rmd

I downloaded the most recent Bioconductor docker 'devel' image

```{sh}
$ docker pull bioconductor/bioconductor_docker:devel
```

The Bioconductor docker container does not contain valgrind. Start by installing it

```{sh}
$ docker run -it --rm bioconductor/bioconductor_docker:devel bash
root@aebe3fe17883:/# apt-get update && apt-get install valgrind
```

Install package(s) to be tested.

```{sh}
root@aebe3fe17883:/# R -e "BiocManager::install('IRanges')"
```

Run suspect code under valgrind

```{sh}
root@aebe3fe17883:/# R -d valgrind -e "IRanges::IRanges(1:622e6, width=1)"
```

The first time I ran this code I saw

```{r}
> IRanges::IRanges(1:622e6, width=1)
==662== Warning: set address range perms: large range [0x59c9d040, 0xee15ae70) (undefined)
==662== Warning: set address range perms: large range [0xee15b040, 0x182618e70) (undefined)
==662== Warning: set address range perms: large range [0x182619040, 0x216ad6e70) (undefined)
KILLED
```

This is unusual, and likely indicates that I ran out of memory in my docker environment. I
updated the amount of memory available to docker (via the menu bar icon  'Preferences...'
on my mac) to 20 GB. Re-running, there were, in this case, no errors:

```{r}
> IRanges::IRanges(1:622e6, width=1)
==662== Warning: set address range perms: large range [0x59c9d040, 0xee15ae70) (undefined)
==662== Warning: set address range perms: large range [0xee15b040, 0x182618e70) (undefined)
==662== Warning: set address range perms: large range [0x182619040, 0x216ad6e70) (undefined)
==662== Warning: set address range perms: large range [0x216ad7040, 0x2aaf94e70) (undefined)
==662== Warning: set address range perms: large range [0x182619028, 0x216ad6e88) (noaccess)
IRanges object with 622000000 ranges and 0 metadata columns:
                  start       end     width
              <integer> <integer> <integer>
          [1]         1         1         1
          [2]         2         2         1
          [3]         3         3         1
          [4]         4         4         1
          [5]         5         5         1
          ...       ...       ...       ...
  [621999996] 621999996 621999996         1
  [621999997] 621999997 621999997         1
  [621999998] 621999998 621999998         1
  [621999999] 621999999 621999999         1
  [622000000] 622000000 622000000         1
>
>
==662==
==662== HEAP SUMMARY:
==662==     in use at exit: 7,622,106,694 bytes in 38,024 blocks
==662==   total heap usage: 151,275 allocs, 113,251 frees, 10,307,180,279 bytes allocated
==662==
==662== LEAK SUMMARY:
==662==    definitely lost: 0 bytes in 0 blocks
==662==    indirectly lost: 0 bytes in 0 blocks
==662==      possibly lost: 0 bytes in 0 blocks
==662==    still reachable: 7,622,106,694 bytes in 38,024 blocks
==662==                       of which reachable via heuristic:
==662==                         newarray           : 4,264 bytes in 1 blocks
==662==         suppressed: 0 bytes in 0 blocks
==662== Rerun with --leak-check=full to see details of leaked memory
==662==
==662== For lists of detected and suppressed errors, rerun with: -s
==662== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
```