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bwlewis / irlba

Fast truncated singular value decompositions
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Error in irlba: object 'C_IRLB' not found #36

Open vdebuen opened 6 years ago

vdebuen commented 6 years ago

Hi

First of all, thank you for this great package!

With version 2.1.2 of package irlba I get the expected result for the attached sparse matrix

> packageVersion('irlba')
[1] '2.1.2'
> Xh <- readRDS('test_fail_irlba_C_IRLB_not_found.rds')
> SVD <- irlba(Xh,20)
> str(SVD)
List of 5
 $ d    : num [1:20] 9.6 8.65 8.53 7.25 6.92 ...
 $ u    : num [1:82, 1:20] 0.01995 0.01768 -0.00259 -0.03284 -0.12891 ...
 $ v    : num [1:90, 1:20] -0.0976 -0.1344 -0.1261 -0.1774 -0.0851 ...
 $ iter : int 6
 $ mprod: int 84

But with 2.3.3 it doesn't return anything and shows an intractable error message for me.

> packageVersion('irlba')
[1] '2.3.3'
> Xh <- readRDS('test_fail_irlba_C_IRLB_not_found.rds')
> SVD <- irlba(Xh,20)
Error in irlba(Xh, 20) : object 'C_IRLB' not found
> str(SVD)
Error in str(SVD) : object 'SVD' not found

Thanks in advance and best regards. Víctor de Buen

test_fail_irlba_C_IRLB_not_found.zip

bwlewis commented 6 years ago

Thanks, investigating now.

bwlewis commented 6 years ago

I get:

library(irlba)
packageVersion('irlba')
## [1] ‘2.3.3’

Xh <- readRDS('test_fail_irlba_C_IRLB_not_found.rds')
SVD <- irlba(Xh,20)
str(SVD)

## List of 5
##  $ d    : num [1:20] 9.6 8.65 8.53 7.25 6.92 ...
##  $ u    : num [1:82, 1:20] -0.01995 -0.01768 0.00259 0.03284 0.12891 ...
##  $ v    : num [1:90, 1:20] 0.0976 0.1344 0.1261 0.1774 0.0851 ...
##  $ iter : int 5
##  $ mprod: int 86

Can you report your R.version output? Also, do things work for you with the current stable version on CRAN (2.3.2) -- I highly recommend sticking with the CRAN version instead of GitHub if possible.

vdebuen commented 6 years ago

Thank you for your quick response.

> R.Version()
$platform
[1] "x86_64-w64-mingw32"

$arch
[1] "x86_64"

$os
[1] "mingw32"

$system
[1] "x86_64, mingw32"

$status
[1] ""

$major
[1] "3"

$minor
[1] "4.4"

$year
[1] "2018"

$month
[1] "03"

$day
[1] "15"

$`svn rev`
[1] "74408"

$language
[1] "R"

$version.string
[1] "R version 3.4.4 (2018-03-15)"

$nickname
[1] "Someone to Lean On"

I wanted to try out the new version to calculate the smallest eigenvalues as well.

I'm going to try different versions of R on other linux machines I have access to.

vdebuen commented 6 years ago

It works fine in all combinations of linux 64 - R Version - irlba version which I've checked:

bwlewis commented 6 years ago

FYI the smallest eigenvalue option is available in the stable version on CRAN.

I'll try to reproduce on a windows machine. Unfortunately I don't have ready access to one -- but I can go through the winbuilder to run checks on the package at least.

On 6/20/18, vdebuen notifications@github.com wrote:

It works fine in all combinations of linux 64 - R Version - irlba version which I've checked:

  • With Linux-64 R version 3.3.2 (2016-10-31), irlba 2.3.3 works fine
  • With Linux-64 R version 3.4.2 (2017-09-28), irlba 2.2.1 works fine
  • With Linux-64 R version 3.4.2 (2017-09-28), irlba 2.3.3 works fine
  • With Linux-64 R version 3.4.3 (2017-11-30), irlba 2.3.1 works fine
  • With Linux-64 R version 3.4.3 (2017-11-30), irlba 2.3.3 works fine

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/bwlewis/irlba/issues/36#issuecomment-398707398

vdebuen commented 6 years ago

Sorry but I don't view the "smallest" argument in CRAN version

> packageVersion('irlba')
 [1] ‘2.1.2’
> args('irlba')
 function (A, nv = 5, nu, maxit = 1000, work = nv + 7, reorth = TRUE, 
     tol = 0.00001, v = NULL, right_only = FALSE, verbose = FALSE, 
     scale, center, du, ds, dv, shift, mult, fastpath = TRUE)

I forgot to mention that I have Microsoft R Open installed in Windows.

bwlewis commented 6 years ago

the current cran version is 2.3.2, see

https://cran.r-project.org/web/packages/irlba/index.html

not sure why you've got such an old version?

On Thu, Jun 21, 2018, 11:48 vdebuen notifications@github.com wrote:

Sorry but I don't view the "smallest" argument in CRAN version

packageVersion('irlba') [1] ‘2.1.2’ args('irlba') function (A, nv = 5, nu, maxit = 1000, work = nv + 7, reorth = TRUE, tol = 0.00001, v = NULL, right_only = FALSE, verbose = FALSE, scale, center, du, ds, dv, shift, mult, fastpath = TRUE)

I forgot to mention that I have Microsoft R Open https://mran.microsoft.com/open installed in Windows.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bwlewis/irlba/issues/36#issuecomment-399151286, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIsntNPmttezEz1R0q3e6T4OsQYnFwXks5t-8BqgaJpZM4UuAx5 .

bwlewis commented 5 years ago

Any update on this? Were you able to get things to work?

FYI a new release is pending, will be on CRAN soon...

vdebuen commented 5 years ago

Finally I updated R and all the packages and everything worked again without problems. When the new version is ready I will try it without a doubt. Thank you very much for your help and interest.