Issue with bbml

[SROY19930311]

I am getting this error while running bbdml

Error: object 'matrixOps' not found whilst loading namespace 'slam'

Please help.

[adw96]

Hello — in order to help you we need more information. Please provide further details including a sessionInfo(), confirmation that you can run the examples, and the code that’s causing issues. Cheers, Amy

[SROY19930311]

Hello, Here is the session info:

sessionInfo() R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS 14.2.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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] magrittr_2.0.3 phyloseq_1.38.0 corncob_0.4.1

loaded via a namespace (and not attached): [1] backports_1.4.1 plyr_1.8.8 igraph_1.3.5 splines_4.1.1
[5] GenomeInfoDb_1.30.1 ggplot2_3.5.1 foreach_1.5.2 fansi_1.0.3
[9] checkmate_2.1.0 cluster_2.1.4 remotes_2.5.0 Biostrings_2.62.0
[13] colorspace_2.0-3 dplyr_1.1.4 callr_3.7.6 crayon_1.5.2
[17] RCurl_1.98-1.9 jsonlite_1.8.8 survival_3.4-0 iterators_1.0.14
[21] ape_5.6-2 glue_1.6.2 registry_0.5-1 gtable_0.3.5
[25] zlibbioc_1.40.0 XVector_0.34.0 pkgbuild_1.4.4 Rhdf5lib_1.16.0
[29] BiocGenerics_0.40.0 scales_1.3.0 Rcpp_1.0.11 stats4_4.1.1
[33] pkgconfig_2.0.3 utf8_1.2.2 tidyselect_1.2.0 rlang_1.1.3
[37] reshape2_1.4.4 munsell_0.5.1 tools_4.1.1 cli_3.6.1
[41] generics_0.1.3 ade4_1.7-20 biomformat_1.22.0 stringr_1.5.1
[45] processx_3.8.0 nlme_3.1-160 compiler_4.1.1 rstudioapi_0.14
[49] curl_5.2.1 tibble_3.2.1 stringi_1.7.8 ps_1.7.2
[53] desc_1.4.3 forcats_1.0.0 lattice_0.20-45 Matrix_1.5-1
[57] vegan_2.6-4 permute_0.9-7 multtest_2.50.0 vctrs_0.6.5
[61] trust_0.1-8 pillar_1.9.0 lifecycle_1.0.4 rhdf5filters_1.6.0
[65] data.table_1.14.4 bitops_1.0-7 R6_2.5.1 IRanges_2.28.0
[69] codetools_0.2-18 MASS_7.3-58.1 rhdf5_2.38.1 S4Vectors_0.32.4
[73] GenomeInfoDbData_1.2.7 mgcv_1.8-41 parallel_4.1.1 grid_4.1.1
[77] Biobase_2.54.0

###################### I could run the example file with no covariates but not with covariate DayAmdmt. This problem also exists when I run the same code with my data.

corncob <- bbdml(formula = OTU.1 ~ DayAmdmt,

• phi.formula = ~ DayAmdmt,
• data = soil) Error: object 'matrixOps' not found whilst loading namespace 'slam'

[adw96]

I’m going to assign @svteichman and @gthopkins to help you out. Sarah, would you mind leading this (Grant’s quals are Friday, but I want him to take over this stuff soon). Thanks, to both of you!

[svteichman]

Sounds good! I'll start looking into it, and if it takes me longer than the end of the week I'll pass it off to Grant with my thoughts on it.

[svteichman]

Hi @SROY19930311,

Could you please tell me the output of running the following code in your console: packageVersion("slam").

If the result is not 0.1-50 through 0.1-52, could you try removing the slam package and reinstalling it? You can do this with the functions remove.packages("slam") and install.packages("slam"). After doing this, can you confirm that you still run into this error?

I am not able to reproduce this error on my personal computer, which suggests to me that it is an issue with one of the dependencies for corncob. If this approach doesn't help, then we can consider other options.

Best, Sarah

[SROY19930311]

Dear Sarah,

packageVersion("slam") [1] ‘0.1.52’

I then removed the package and tried to reinstall it. It says this: Warning in install.packages : installation of package ‘slam’ had non-zero exit status

I then downloaded the package from CRAN and installed it manually from the Zip folder I downloaded.

The problem still persists.

Thank you Shamik

[svteichman]

@SROY19930311, when you run packageVersion("slam"), what do you get?

[SROY19930311]

I get this

packageVersion("slam") [1] ‘0.1.52’

[svteichman]

@SROY19930311 What version of R do you have? What is the result when you type version in R? From checking the namespace of slam it seems that matrixOps is only created for R version 4.3.0 and later. If you have an earlier version, I'd suggest updating R and then trying again.

@adw96, if this is indeed the problem, do you think that we should update the version of R that corncob depends on? Right now it is "Depends: R (>= 3.2)".

[adw96]

Thanks, @svteichman -- what functionality uses slam? ie how essential is the dependency?

[svteichman]

@adw96 I'll look into it! It's not one of our dependencies, so I imagine it's a dependency of a dependency, and it appears to come up when we put covariates into the bbdml() function. But I can look a little deeper into which of the functions that we call, calls this matrixOps class.

[SROY19930311]

Hello, This is my R version "R version 4.1.1 (2021-08-10)". If the problem is resolved with my current R-version. I would want that. I have other packages that might not work with R 4.3.0. Let me know your thoughts.

Thank you Shamik

[svteichman]

In that case, I'm going to tag @gthopkins. @gthopkins, when you get the chance, do you mind looking into which dependency is using the matrixObs class from bbdml(), and see if there is a workaround for previous versions of R?

[gthopkins]

@svteichman Yes, I will take the lead on this!

[gthopkins]

@SROY19930311 we have attempted to fix this error in pull request #178 by removing our dependence on the slam package. Please re-install corncob and let us know if this resolves your error when you use the bbdml() function.