yiluheihei
commented
2 years ago Thanks for your interested in microbiomeMarker. This is because there are two class named phylo, you can just ignore it. And you can try options(getClass.msg=FALSE) to see whether it can get rid of the annoying message. Your comments and suggestions are welcome
If you think this project is helpful to you, you can give this project a star ⭐. Thanks.
Hello - when using the microbiomeMarker package, I am receiving the above message whenever using functions from either the microbiomeMarker or phyloseq packages. When running more intensive functions, such as phyloseq::tax_glom, the message is printed thousands of times, making the output difficult to parse. I realize this issue has been raised in the past and resolved, but I am still experiencing the issue using a more recent version of microbiomeMarker. Any help would be greatly appreciated. Here's a minimal reproducible example - please let me know if I can provide more information.
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] microbiomeMarker_1.0.2 phyloseq_1.38.0
loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_2.0-3 ggtree_3.2.1
[4] rjson_0.2.21 ellipsis_0.3.2 circlize_0.4.14
[7] XVector_0.34.0 GenomicRanges_1.46.1 GlobalOptions_0.1.2
[10] aplot_0.1.2 clue_0.3-60 rstudioapi_0.13
[13] bit64_4.0.5 AnnotationDbi_1.56.2 fansi_1.0.2
[16] codetools_0.2-18 splines_4.1.3 doParallel_1.0.17
[19] cachem_1.0.6 geneplotter_1.72.0 plotROC_2.2.1
[22] ade4_1.7-18 jsonlite_1.8.0 nloptr_2.0.0
[25] annotate_1.72.0 cluster_2.1.2 png_0.1-7
[28] compiler_4.1.3 httr_1.4.2 lazyeval_0.2.2
[31] assertthat_0.2.1 Matrix_1.4-0 fastmap_1.1.0
[34] limma_3.50.1 cli_3.2.0 tools_4.1.3
[37] igraph_1.2.11 gtable_0.3.0 glue_1.6.2
[40] GenomeInfoDbData_1.2.7 reshape2_1.4.4 dplyr_1.0.8
[43] Rcpp_1.0.8.3 Biobase_2.54.0 vctrs_0.3.8
[46] Biostrings_2.62.0 rhdf5filters_1.6.0 multtest_2.50.0
[49] ape_5.6-2 nlme_3.1-155 iterators_1.0.14
[52] ANCOMBC_1.4.0 stringr_1.4.0 rbibutils_2.2.7
[55] lifecycle_1.0.1 gtools_3.9.2 XML_3.99-0.9
[58] zlibbioc_1.40.0 MASS_7.3-55 scales_1.1.1
[61] MatrixGenerics_1.6.0 parallel_4.1.3 SummarizedExperiment_1.24.0 [64] biomformat_1.22.0 metagenomeSeq_1.36.0 rhdf5_2.38.1
[67] RColorBrewer_1.1-2 yaml_2.3.5 ComplexHeatmap_2.10.0
[70] memoise_2.0.1 ggplot2_3.3.5 ggfun_0.0.5
[73] yulab.utils_0.0.4 stringi_1.7.6 RSQLite_2.2.10
[76] genefilter_1.76.0 S4Vectors_0.32.3 foreach_1.5.2
[79] tidytree_0.3.9 permute_0.9-7 caTools_1.18.2
[82] BiocGenerics_0.40.0 BiocParallel_1.28.3 shape_1.4.6
[85] GenomeInfoDb_1.30.1 Rdpack_2.1.4 rlang_1.0.2
[88] pkgconfig_2.0.3 matrixStats_0.61.0 bitops_1.0-7
[91] Wrench_1.12.0 lattice_0.20-45 purrr_0.3.4
[94] Rhdf5lib_1.16.0 treeio_1.18.1 patchwork_1.1.1
[97] bit_4.0.4 tidyselect_1.1.2 plyr_1.8.6
[100] magrittr_2.0.2 DESeq2_1.34.0 R6_2.5.1
[103] gplots_3.1.1 IRanges_2.28.0 generics_0.1.2
[106] DelayedArray_0.20.0 DBI_1.1.2 pillar_1.7.0
[109] mgcv_1.8-39 survival_3.3-1 KEGGREST_1.34.0
[112] RCurl_1.98-1.6 tibble_3.1.6 crayon_1.5.0
[115] KernSmooth_2.23-20 utf8_1.2.2 microbiome_1.16.0
[118] GetoptLong_1.0.5 locfit_1.5-9.5 grid_4.1.3
[121] data.table_1.14.2 blob_1.2.2 vegan_2.5-7
[124] digest_0.6.29 xtable_1.8-4 tidyr_1.2.0
[127] gridGraphics_0.5-1 glmnet_4.1-3 stats4_4.1.3
[130] munsell_0.5.0 ggplotify_0.1.0