seqDist crashes on Mac

[Julian Zhou]

This is driving me nuts! R Session aborted as soon as I call seqDist ("R encountered a fatal error"). No explanation/error message whatsoever reported.

> library(alakazam)
Loading required package: ggplot2
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] alakazam_0.2.6.999 ggplot2_2.2.1     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10     dplyr_0.5.0      assertthat_0.2.0 grid_3.4.0       plyr_1.8.4       R6_2.2.1        
 [7] gtable_0.2.0     DBI_0.6-1        magrittr_1.5     scales_0.4.1     stringi_1.1.5    lazyeval_0.2.0  
[13] seqinr_3.3-6     tools_3.4.0      ade4_1.7-6       readr_1.1.0      igraph_1.0.1     munsell_0.4.3   
[19] hms_0.3          compiler_3.4.0   colorspace_1.3-2 tibble_1.3.0    

> seqDist("ATGGC", "ATGGG")

[Julian Zhou]

Can someone else please try this on their Mac(s) too? Just to make certain that it's a reproducible issue and not just my Mac. It's definitely reproducible on my Mac, and only started happening like 2 days ago (but I didn't do anything extraordinary!?)

[Jason Vander Heiden]

> devtools::install_bitbucket("kleinstein/alakazam@default")
> library(alakazam)
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] alakazam_0.2.6.999 ggplot2_2.2.1     

loaded via a namespace (and not attached):
 [1] igraph_1.0.1     Rcpp_0.12.10     knitr_1.14       magrittr_1.5     hms_0.3          devtools_1.12.0  munsell_0.4.3   
 [8] colorspace_1.3-2 R6_2.1.2         httr_1.1.0       plyr_1.8.4       dplyr_0.5.0      tools_3.2.3      grid_3.2.3      
[15] gtable_0.2.0     DBI_0.6-1        seqinr_3.3-6     git2r_0.13.1     withr_1.0.1      ade4_1.7-6       lazyeval_0.2.0  
[22] assertthat_0.1   digest_0.6.9     tibble_1.2       readr_1.1.0      curl_0.9.6       memoise_1.0.0    stringi_1.1.5   
[29] scales_0.4.1    
> seqDist("ATGGC", "ATGGG")
[1] 1

Works for me, but we aren't on the same OS or R versions.

[Julian Zhou]

I wonder if I should try reverting back to R 3.2.3. The only thing major that changed since I last ran this code, as far as I could recall, was R..

[Julian Zhou]

For R 3.4.0:

"Important: this release uses Clang 4.0.0 and GNU Fortran 6.1, neither of which is supplied by Apple. If you wish to compile R packages from sources, you will need to download and install those tools - see the tools directory."

Hmm

[Jason Vander Heiden]

Hard to say if it's your system for a version incompatibility without more testing. I would try uninstalling R and RStudio, deleting whatever directories they leave behind, and reinstalling.

[Jason Vander Heiden]

Ah... Maybe it's the clang/fortran thing then.

[Julian Zhou]

Naked R (i.e. not RStudio) gives more informative error message:

> library(alakazam)
Loading required package: ggplot2
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] alakazam_0.2.6.999 ggplot2_2.2.1     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10     dplyr_0.5.0      assertthat_0.2.0 grid_3.4.0      
 [5] plyr_1.8.4       R6_2.2.1         gtable_0.2.0     DBI_0.6-1       
 [9] magrittr_1.5     scales_0.4.1     stringi_1.1.5    lazyeval_0.2.0  
[13] seqinr_3.3-6     tools_3.4.0      ade4_1.7-6       readr_1.1.0     
[17] munsell_0.4.3    igraph_1.0.1     hms_0.3          compiler_3.4.0  
[21] colorspace_1.3-2 tibble_1.3.0    
> seqDist("acca", "acct")

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call("alakazam_seqDistRcpp", PACKAGE = "alakazam", seq1, seq2,     dist_mat)
 2: seqDistRcpp(seq1, seq2, dist_mat)
 3: seqDist("acca", "acct")

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: 

[Julian Zhou]

OK this appears to be an R thing. Reverting back to R 3.3.3 from R 3.4.0 solved the issue for me (seqDist at least).

With R 3.4.0., tried installing gfortran 6.1 and clang4.0.0, in addition to following extra instructions at https://cran.r-project.org/bin/macosx/tools/, nada!