Entering edit mode
Hi
I'm trying to run old code with a new version of R/bioconductor and it fails on phyloseq_to_DESeq2
Any thoughts?
Thanks
> phyloseq_to_deseq2(physeq, ~ Day)
converting counts to integer mode
Error in Validateobject(.object) : invalid class "DESeqDataSet" object:
'NAMES' slot must be set to NULL at all time
> sessionInfo()
R version 4.5.0 (2025-04-11 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_Israel.utf8 LC_CTYPE=English_Israel.utf8 LC_MONETARY=English_Israel.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Israel.utf8
time zone: Asia/Jerusalem
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_5.8-1 RColorBrewer_1.1-3 viridis_0.6.5 viridisLite_0.4.2
[5] circlize_0.4.16 ComplexHeatmap_2.24.0 ashr_2.2-63 apeglm_1.30.0
[9] DESeq2_1.48.0 SummarizedExperiment_1.39.0 Biobase_2.68.0 MatrixGenerics_1.20.0
[13] matrixStats_1.5.0 GenomicRanges_1.60.0 GenomeInfoDb_1.44.0 IRanges_2.42.0
[17] S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.4 lsmeans_2.30-2
[21] emmeans_1.11.1 lmtest_0.9-40 zoo_1.8-14 kableExtra_1.4.0
[25] knitr_1.50 DT_0.33 betareg_3.2-2 ggrepel_0.9.6
[29] scales_1.4.0 compositions_2.0-8 nlme_3.1-168 plotly_4.10.4
[33] phyloseq_1.52.0 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[37] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[41] tibble_3.2.1 ggplot2_3.5.2 tidyverse_2.0.0 qiime2R_0.99.6
loaded via a namespace (and not attached):
[1] tensorA_0.36.2.1 rstudioapi_0.17.1 jsonlite_2.0.0 shape_1.4.6.1 magrittr_2.0.3
[6] estimability_1.5.1 NADA_1.6-1.1 modeltools_0.2-24 farver_2.1.2 rmarkdown_2.29
[11] GlobalOptions_0.1.2 vctrs_0.6.5 multtest_2.64.0 SQUAREM_2021.1 base64enc_0.1-3
[16] mixsqp_0.3-54 htmltools_0.5.8.1 S4Arrays_1.8.0 truncnorm_1.0-9 Rhdf5lib_1.30.0
[21] SparseArray_1.8.0 Formula_1.2-5 rhdf5_2.52.0 htmlwidgets_1.6.4 plyr_1.8.9
[26] sandwich_3.1-1 igraph_2.1.4 lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[31] Matrix_1.7-3 R6_2.6.1 fastmap_1.2.0 GenomeInfoDbData_1.2.14 clue_0.3-66
[36] numDeriv_2016.8-1.1 digest_0.6.37 colorspace_2.1-1 irlba_2.3.5.1 Hmisc_5.2-3
[41] vegan_2.6-10 labeling_0.4.3 invgamma_1.1 timechange_0.3.0 httr_1.4.7
[46] abind_1.4-8 mgcv_1.9-3 compiler_4.5.0 bit64_4.6.0-1 withr_3.0.2
[51] doParallel_1.0.17 htmlTable_2.4.3 backports_1.5.0 BiocParallel_1.42.0 MASS_7.3-65
[56] bayesm_3.1-6 DelayedArray_0.34.1 rjson_0.2.23 biomformat_1.37.0 permute_0.9-7
[61] tools_4.5.0 foreign_0.8-90 nnet_7.3-20 glue_1.8.0 rhdf5filters_1.20.0
[66] checkmate_2.3.2 cluster_2.1.8.1 reshape2_1.4.4 ade4_1.7-23 gtable_0.3.6
[71] tzdb_0.5.0 data.table_1.17.0 hms_1.1.3 xml2_1.3.8 XVector_0.48.0
[76] flexmix_2.3-20 foreach_1.5.2 pillar_1.10.2 vroom_1.6.5 emdbook_1.3.13
[81] robustbase_0.99-4-1 splines_4.5.0 lattice_0.22-7 bit_4.6.0 survival_3.8-3
[86] tidyselect_1.2.1 locfit_1.5-9.12 Biostrings_2.76.0 gridExtra_2.3 bookdown_0.43
[91] svglite_2.1.3 zCompositions_1.5.0-4 xfun_0.52 DEoptimR_1.1-3-1 stringi_1.8.7
[96] UCSC.utils_1.5.0 lazyeval_0.2.2 yaml_2.3.10 evaluate_1.0.3 codetools_0.2-20
[101] bbmle_1.0.25.1 cli_3.6.5 rpart_4.1.24 xtable_1.8-4 systemfonts_1.2.3
[106] Rcpp_1.0.14 coda_0.19-4.1 png_0.1-8 bdsmatrix_1.3-7 parallel_4.5.0
[111] mvtnorm_1.3-3 crayon_1.5.3 GetoptLong_1.0.5 rlang_1.1.6
