sparse matrix - R Error in validObject(.Object) when running as script, but not in console -


the following code works fine in r console (r 3.3.0):

m = system.file("external/pores_1.mtx", package = "matrix") x = matrix::readmm(m)

i can put in script , runs fine in r console as:

source("test.r")

however, when execute rscript --vanilla test.r or rscript test.r, error:

error in validobject(.object) :    invalid class “dgtmatrix” object: not valid 'mnumeric' class object calls: <anonymous> -> new -> initialize -> initialize -> validobject execution halted

i don't know if related specific function. guessing has how rscript works, used various other libraries , functions , have never seen this. idea happening?

i can confirm ... i'm getting exact same error when running script containing call glmnet(). able trace matrix package, on glmnet depends.

i back-rev'd r version v3.3.3 -> v3.3.2 , error disappeared. checked sessioninfo() between 2 , discovered version of matrix package differed ... 1.2-8 (in v3.3.3) , 1.2-7.1 (in v3.3.2). confirm, replaced "ok" version of matrix (7.1) "broken" version , error returned.

i can confirm explicitly loading methods package via library(methods) resolves error (somehow?), explains differing behavior between console call , rscript call command line.

so, appears have 2 work-arounds:

  1. library(methods)
  2. back rev version of matrix 1.2-7.1.

neither super satisfactory ... i'd know what's going on matrix 1.2-8. maybe it'll bug-fixed in next version.

if you're interested, here sessioninfo():

r version 3.3.3 (2017-03-06) platform: x86_64-pc-linux-gnu (64-bit) running under: ubuntu 16.04.2 lts  locale:  [1] lc_ctype=en_us.utf-8       lc_numeric=c                [3] lc_time=en_us.utf-8        lc_collate=en_us.utf-8      [5] lc_monetary=en_us.utf-8    lc_messages=en_us.utf-8     [7] lc_paper=en_us.utf-8       lc_name=c                   [9] lc_address=c               lc_telephone=c             [11] lc_measurement=en_us.utf-8 lc_identification=c         attached base packages: [1] stats     graphics  grdevices utils     datasets  base  other attached packages: [1] glmnet_2.0-5  foreach_1.4.3 matrix_1.2-8   loaded via namespace (and not attached): [1] codetools_0.2-15 grid_3.3.3       iterators_1.0.8  methods_3.3.3     [5] lattice_0.20-35

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