FilterandTrim Issue ("Mnumeric" error)

[sjhardisty]

Hello, I am having an issue with the filter and trim package

Thanks for any help! I've been looking through the forums with no luck so far.

These are the errors (up to 5) encountered in individual cores... Error in validObject(.Object) : invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class Error in validObject(.Object) : invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class Error in validObject(.Object) : invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class Error in validObject(.Object) : invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class Error in validObject(.Object) : invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class In addition: Warning message: In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, : all scheduled cores encountered errors in user code

• R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8

Matrix products: default BLAS: /opt/R/4.0.2/lib64/R/lib/libRblas.so LAPACK: /opt/R/4.0.2/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] dplyr_1.0.6 data.table_1.14.0 e1071_1.7-7 randomForest_4.6-14 caret_6.0-88 ggplot2_3.3.4
[7] glmnet_4.1-1 Matrix_1.3-4 vegan_2.5-7 lattice_0.20-44 permute_0.9-5 dada2_1.16.0
[13] Rcpp_1.0.6 phangorn_2.7.0 ape_5.5 phyloseq_1.32.0

loaded via a namespace (and not attached): [1] colorspace_2.0-1 hwriter_1.3.2 ellipsis_0.3.2 class_7.3-19
[5] rprojroot_2.0.2 XVector_0.28.0 GenomicRanges_1.40.0 fs_1.5.0
[9] rstudioapi_0.13 proxy_0.4-26 remotes_2.4.0 prodlim_2019.11.13
[13] fansi_0.5.0 lubridate_1.7.10 codetools_0.2-18 splines_4.0.2
[17] cachem_1.0.5 knitr_1.33 pkgload_1.2.1 ade4_1.7-16
[21] jsonlite_1.7.2 pROC_1.17.0.1 Rsamtools_2.4.0 cluster_2.1.2
[25] png_0.1-7 compiler_4.0.2 fastmap_1.1.0 assertthat_0.2.1
[29] cli_2.5.0 htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.0.2
[33] igraph_1.2.6 gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.3
[37] reshape2_1.4.4 ShortRead_1.46.0 fastmatch_1.1-0 Biobase_2.48.0
[41] vctrs_0.3.8 Biostrings_2.56.0 multtest_2.44.0 nlme_3.1-152
[45] iterators_1.0.13 timeDate_3043.102 xfun_0.24 gower_0.2.2
[49] stringr_1.4.0 ps_1.6.0 testthat_3.0.2 lifecycle_1.0.0
[53] devtools_2.4.2 zlibbioc_1.34.0 MASS_7.3-54 scales_1.1.1
[57] ipred_0.9-11 hms_1.1.0 parallel_4.0.2 SummarizedExperiment_1.18.2 [61] biomformat_1.16.0 rhdf5_2.32.4 RColorBrewer_1.1-2 memoise_2.0.0
[65] rpart_4.1-15 latticeExtra_0.6-29 stringi_1.6.2 desc_1.3.0
[69] S4Vectors_0.26.1 foreach_1.5.1 BiocGenerics_0.34.0 pkgbuild_1.2.0
[73] BiocParallel_1.22.0 lava_1.6.9 shape_1.4.6 GenomeInfoDb_1.24.2
[77] rlang_0.4.11 pkgconfig_2.0.3 matrixStats_0.59.0 bitops_1.0-7
[81] purrr_0.3.4 Rhdf5lib_1.10.1 GenomicAlignments_1.24.0 recipes_0.1.16
[85] processx_3.5.2 tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1
[89] R6_2.5.0 IRanges_2.22.2 generics_0.1.0 DelayedArray_0.14.1
[93] DBI_1.1.1 pillar_1.6.1 withr_2.4.2 mgcv_1.8-36
[97] survival_3.2-11 RCurl_1.98-1.3 nnet_7.3-16 tibble_3.1.2
[101] crayon_1.4.1 utf8_1.2.1 usethis_2.0.1 jpeg_0.1-8.1
[105] progress_1.2.2 grid_4.0.2 callr_3.7.0 ModelMetrics_1.2.2.2
[109] digest_0.6.27 RcppParallel_5.0.2 stats4_4.0.2 munsell_0.5.0
[113] sessioninfo_1.1.1 quadprog_1.5-8

[benjjneb]

See https://github.com/benjjneb/dada2/issues/1378#issuecomment-881815297

[sjhardisty]

Thanks for the quick response!

For some reason I am still unable to uninstall Matrix or update dada2 on my R (running through a university Rstudio/server).

remove.packages("Matrix", lib="/opt/R/4.0.2/lib64/R/library") Updating HTML index of packages in '.Library' Warning in remove.packages : cannot create file '/opt/R/4.0.2/lib64/R/doc/html/packages.html', reason 'Permission denied' Warning in remove.packages : cannot update HTML package index

After installing matrix 3.2 and trying to load it:

packageVersion("Matrix") [1] ‘1.3.4’

[benjjneb]

Is there any support available through your university IT on how to update R packages on the server you are using? I can't really help with that aspect.