Entering edit mode
hi,
I noticed, when I try to align() and give an output file path which includes a non-existent directory, I get a segfault instead of an error message. Here using development branch, and the example code from the vignette, but adding "foo/" to the output_file argument:
> library(Rsubread)
> ref <- system.file("extdata","reference.fa",package="Rsubread")
> buildindex(basename="reference_index",reference=ref)
> reads <- system.file("extdata","reads.txt.gz",package="Rsubread")
> align(index="reference_index",readfile1=reads,output_file="foo/alignResults.BAM")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 1.19.3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file : /home/love/bin/R/library/Rsubread/extdata/reads.t ... ||
|| Output file : foo/alignResults.BAM (BAM) ||
|| Index name : reference_index ||
|| Phred offset : 33 ||
|| ||
|| Min votes : 3 ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (11-Sep-2015 10:06:38) ======================\\
|| ||
|| Decompress /home/love/bin/R/library/Rsubread/extdata/reads.txt.gz... ||
|| The input file contains base space reads. ||
|| WARNING The specified phred-score offset (33) seems to be incorrect. ||
|| The observed phred-score range is [66,98]. ||
|| ||
*** caught segfault ***
address 0x8, cause 'memory not mapped'
Traceback:
1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")
2: align(index = "reference_index", readfile1 = reads, output_file = "foo/alignResults.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:
> sessionInfo()
R Under development (unstable) (2015-06-21 r68565)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 15.04
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 datasets utils methods base
other attached packages:
[1] Rsubread_1.19.3
loaded via a namespace (and not attached):
[1] compiler_3.3.0 tools_3.3.0
