Subsetting shenanigans

[PeteHaitch]

Something funky seems to be going on with subsetting:

library(spm)
m <- 10000
n <- 2500
x <- matrix(rnorm(m*n), m, n)
xs = mat2spm(x)
xs[1:10, 1:5] # works
xs[1:5, 1:10] # works
xs[1:10, 1:10] # wut?
# An spm (single precision matrix): 10x10
Error in dim(submat) <- c(toprow, topcol) :
  dims [product 50] do not match the length of object [100]

Any ideas?

[wrathematics]

I think it's the print method. It's a bit of a mess. I'll take a look soon.

[wrathematics]

Should be fixed in the latest push. Still a bit of a mess though 🙂

[PeteHaitch]

Having some troubles installing after update, sorry

> install_github("wrathematics/spm")
Using GitHub PAT from envvar GITHUB_PAT
Downloading GitHub repo wrathematics/spm@master
from URL https://api.github.com/repos/wrathematics/spm/zipball/master
Installing spm
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/f1/6pjy5xbn0_9_7xwq6l7fj2yc0000gn/T/Rtmp8jIoQu/devtools167ce13f57ad/wrathematics-spm-b8c071d'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *source* package ‘spm’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
** libs
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c bracket.c -o bracket.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c chol.c -o chol.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c converters.c -o converters.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c crossprod.c -o crossprod.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c diag.c -o diag.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c dims.c -o dims.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c isSymmetric.c -o isSymmetric.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c matmult.c -o matmult.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c solve.c -o solve.o
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c xpose.c -o xpose.o
/usr/local/clang4/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o spm.so bracket.o chol.o converters.o crossprod.o diag.o dims.o isSymmetric.o matmult.o solve.o xpose.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/spm/libs
** R
** tests
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘crossprod’ from package ‘base’ in package ‘spm’
Creating a generic function for ‘tcrossprod’ from package ‘base’ in package ‘spm’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘spm’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘spm’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘spm’
Creating a generic function for ‘object.size’ from package ‘utils’ in package ‘spm’
** help
No man pages found in package  ‘spm’
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘spm’ in FUN(X[[i]], ...):
 no such symbol R_numbytes_spm in package /Library/Frameworks/R.framework/Versions/3.4/Resources/library/spm/libs/spm.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/spm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/spm’
Installation failed: Command failed (1)

> sessionInfo()
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

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_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] colorout_1.1-2    repete_0.0.0.9008 devtools_1.13.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12            XVector_0.17.0          magrittr_1.5
 [4] GenomicRanges_1.29.10   BiocGenerics_0.23.0     zlibbioc_1.23.0
 [7] IRanges_2.11.12         munsell_0.4.3           colorspace_1.3-2
[10] R6_2.2.2                httr_1.2.1.9000         stringr_1.2.0
[13] GenomeInfoDb_1.13.4     plyr_1.8.4              tools_3.4.0
[16] parallel_3.4.0          git2r_0.19.0            withr_1.0.2
[19] fortunes_1.5-4          digest_0.6.12           GenomeInfoDbData_0.99.1
[22] pryr_0.1.2              S4Vectors_0.15.5        bitops_1.0-6
[25] codetools_0.2-15        curl_2.8.1              RCurl_1.95-4.8
[28] memoise_1.1.0           stringi_1.1.5           compiler_3.4.0
[31] scales_0.4.1            stats4_3.4.0

[wrathematics]

Sorry about that; forgot to add a file in the commit. Have too many uncommitted changes in the repo at the moment.

I think it should be fixed now. Travis currently shows the build erroring, but it's from R CMD check warnings. Let me know if it doesn't compile.

[PeteHaitch]

Thanks, back in business with successful compilation. I did get several gfortran warnings (macOS) but no idea if they matter. Can post details if you'd like

[wrathematics]

Please do! If you could paste your whole output starting from checking for gcc... (in a new issue?) that would be helpful.

I suspect it's compiling single precision blas/lapack for you (finally added this morning), but you didn't need it before, so that's really a bug...

Thanks!