lshep
commented
3 years ago What is your sessionInfo ? This Should be fixed in recent versions of Bioconductor. If you updated to a recent version the error should not persist
Closed CQgit closed 3 years ago
lshep
commented
3 years ago What is your sessionInfo ? This Should be fixed in recent versions of Bioconductor. If you updated to a recent version the error should not persist
lshep
commented
3 years ago See also this post on the support site https://support.bioconductor.org/p/p132709/#p133562
CQgit
commented
3 years ago sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.16
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_2.0.0 heatmaply_1.1.1 viridis_0.5.1
[6] viridisLite_0.3.0 RColorBrewer_1.1-2 gplots_3.1.1 plotly_4.9.3 gt_0.2.2
[11] DT_0.17 enrichplot_1.6.1 msigdbr_7.2.1 clusterProfiler_3.14.3 gprofiler2_0.2.0
[16] GSVA_1.34.0 GSEABase_1.48.0 graph_1.64.0 annotate_1.64.0 XML_3.99-0.3
[21] AnnotationFilter_1.10.0 GenomicFeatures_1.38.2 AnnotationDbi_1.48.0 Biobase_2.46.0 GenomicRanges_1.38.0
[26] GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0 tximport_1.14.2
[31] edgeR_3.28.1 limma_3.42.2 matrixStats_0.57.0 cowplot_1.1.1 forcats_0.5.0
[36] stringr_1.4.0 dplyr_1.0.3 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[41] tibble_3.0.5 ggplot2_3.3.3 tidyverse_1.3.0 tinytex_0.28 knitr_1.30
[46] rmarkdown_2.6
loaded via a namespace (and not attached):
[1] pacman_0.5.1 tidyselect_1.1.0 RSQLite_2.2.2 htmlwidgets_1.5.3
[5] TSP_1.1-10 grid_3.6.3 BiocParallel_1.20.1 munsell_0.5.0
[9] codetools_0.2-18 withr_2.3.0 colorspace_2.0-0 GOSemSim_2.12.1
[13] rstudioapi_0.13 DOSE_3.12.0 labeling_0.4.2 urltools_1.7.3
[17] GenomeInfoDbData_1.2.2 polyclip_1.10-0 bit64_4.0.5 farver_2.0.3
[21] vctrs_0.3.6 generics_0.1.0 xfun_0.20 R6_2.5.0
[25] graphlayouts_0.7.1 seriation_1.2-9 locfit_1.5-9.4 bitops_1.0-6
[29] fgsea_1.12.0 gridGraphics_0.5-1 DelayedArray_0.12.3 assertthat_0.2.1
[33] promises_1.1.1 scales_1.1.1 ggraph_2.0.4 gtable_0.3.0
[37] tidygraph_1.2.0 rlang_0.4.10 splines_3.6.3 rtracklayer_1.46.0
[41] lazyeval_0.2.2 broom_0.7.3 europepmc_0.4 BiocManager_1.30.10
[45] yaml_2.2.1 reshape2_1.4.4 modelr_0.1.8 crosstalk_1.1.1
[49] backports_1.2.1 httpuv_1.5.5 qvalue_2.18.0 tools_3.6.3
[53] ggplotify_0.0.5 ellipsis_0.3.1 ggridges_0.5.3 Rcpp_1.0.6
[57] plyr_1.8.6 progress_1.2.2 zlibbioc_1.32.0 RCurl_1.98-1.2
[61] prettyunits_1.1.1 openssl_1.4.3 SummarizedExperiment_1.16.1 haven_2.3.1
[65] ggrepel_0.9.0 fs_1.5.0 magrittr_2.0.1 data.table_1.13.6
[69] DO.db_2.9 triebeard_0.3.0 reprex_0.3.0 ProtGenerics_1.18.0
[73] hms_1.0.0 mime_0.9 evaluate_0.14 xtable_1.8-4
[77] readxl_1.3.1 gridExtra_2.3 compiler_3.6.3 biomaRt_2.42.1
[81] KernSmooth_2.23-18 crayon_1.3.4 htmltools_0.5.1 later_1.1.0.1
[85] geneplotter_1.64.0 lubridate_1.7.9.2 DBI_1.1.1 tweenr_1.0.1
[89] MASS_7.3-53 rappdirs_0.3.1 Matrix_1.3-2 cli_2.2.0
[93] igraph_1.2.6 pkgconfig_2.0.3 registry_0.5-1 rvcheck_0.1.8
[97] GenomicAlignments_1.22.1 foreach_1.5.1 xml2_1.3.2 webshot_0.5.2
[101] XVector_0.26.0 rvest_0.3.6 digest_0.6.27 Biostrings_2.54.0
[105] cellranger_1.1.0 fastmatch_1.1-0 dendextend_1.14.0 curl_4.3
[109] shiny_1.5.0 Rsamtools_2.2.3 gtools_3.8.2 lifecycle_0.2.0
[113] jsonlite_1.7.2 askpass_1.1 fansi_0.4.2 pillar_1.4.7
[117] lattice_0.20-41 fastmap_1.0.1 httr_1.4.2 GO.db_3.10.0
[121] interactiveDisplayBase_1.24.0 glue_1.4.2 iterators_1.0.13 shinythemes_1.1.2
[125] BiocVersion_3.10.1 bit_4.0.4 ggforce_0.3.2 stringi_1.5.3
[129] blob_1.2.1 caTools_1.18.1 memoise_1.1.0
lshep
commented
3 years ago Yes the recommendation is to upgrade your version of R and Bioconductor. Or look at the support site link for how to downgrade dplyr
CQgit
commented
3 years ago > sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_2.0.0 heatmaply_1.1.1 viridis_0.5.1
[6] viridisLite_0.3.0 RColorBrewer_1.1-2 gplots_3.1.1 plotly_4.9.3 gt_0.2.2
[11] DT_0.17 enrichplot_1.6.1 msigdbr_7.2.1 clusterProfiler_3.14.3 gprofiler2_0.2.0
[16] GSVA_1.34.0 GSEABase_1.48.0 graph_1.64.0 annotate_1.64.0 XML_3.99-0.3
[21] AnnotationFilter_1.10.0 GenomicFeatures_1.38.2 AnnotationDbi_1.48.0 Biobase_2.46.0 GenomicRanges_1.38.0
[26] GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0 tximport_1.14.2
[31] edgeR_3.28.1 limma_3.42.2 matrixStats_0.57.0 cowplot_1.1.1 forcats_0.5.0
[36] stringr_1.4.0 dplyr_1.0.3 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[41] tibble_3.0.5 ggplot2_3.3.3 tidyverse_1.3.0 tinytex_0.28 knitr_1.30
[46] rmarkdown_2.6
loaded via a namespace (and not attached):
[1] pacman_0.5.1 tidyselect_1.1.0 RSQLite_2.2.2 htmlwidgets_1.5.3
[5] TSP_1.1-10 grid_3.6.3 BiocParallel_1.20.1 munsell_0.5.0
[9] codetools_0.2-18 withr_2.3.0 colorspace_2.0-0 GOSemSim_2.12.1
[13] rstudioapi_0.13 DOSE_3.12.0 labeling_0.4.2 urltools_1.7.3
[17] GenomeInfoDbData_1.2.2 polyclip_1.10-0 bit64_4.0.5 farver_2.0.3
[21] vctrs_0.3.6 generics_0.1.0 xfun_0.20 R6_2.5.0
[25] graphlayouts_0.7.1 seriation_1.2-9 locfit_1.5-9.4 bitops_1.0-6
[29] fgsea_1.12.0 gridGraphics_0.5-1 DelayedArray_0.12.3 assertthat_0.2.1
[33] promises_1.1.1 scales_1.1.1 ggraph_2.0.4 gtable_0.3.0
[37] tidygraph_1.2.0 rlang_0.4.10 splines_3.6.3 rtracklayer_1.46.0
[41] lazyeval_0.2.2 broom_0.7.3 europepmc_0.4 BiocManager_1.30.10
[45] yaml_2.2.1 reshape2_1.4.4 modelr_0.1.8 crosstalk_1.1.1
[49] backports_1.2.1 httpuv_1.5.5 qvalue_2.18.0 tools_3.6.3
[53] ggplotify_0.0.5 ellipsis_0.3.1 ggridges_0.5.3 Rcpp_1.0.6
[57] plyr_1.8.6 progress_1.2.2 zlibbioc_1.32.0 RCurl_1.98-1.2
[61] prettyunits_1.1.1 openssl_1.4.3 SummarizedExperiment_1.16.1 haven_2.3.1
[65] ggrepel_0.9.0 fs_1.5.0 magrittr_2.0.1 data.table_1.13.6
[69] DO.db_2.9 triebeard_0.3.0 reprex_0.3.0 ProtGenerics_1.18.0
[73] hms_1.0.0 mime_0.9 evaluate_0.14 xtable_1.8-4
[77] readxl_1.3.1 gridExtra_2.3 compiler_3.6.3 biomaRt_2.42.1
[81] KernSmooth_2.23-18 crayon_1.3.4 htmltools_0.5.1 later_1.1.0.1
[85] geneplotter_1.64.0 lubridate_1.7.9.2 DBI_1.1.1 tweenr_1.0.1
[89] MASS_7.3-53 rappdirs_0.3.1 Matrix_1.3-2 cli_2.2.0
[93] igraph_1.2.6 pkgconfig_2.0.3 registry_0.5-1 rvcheck_0.1.8
[97] GenomicAlignments_1.22.1 foreach_1.5.1 xml2_1.3.2 webshot_0.5.2
[101] XVector_0.26.0 rvest_0.3.6 digest_0.6.27 Biostrings_2.54.0
[105] cellranger_1.1.0 fastmatch_1.1-0 dendextend_1.14.0 curl_4.3
[109] shiny_1.5.0 Rsamtools_2.2.3 gtools_3.8.2 lifecycle_0.2.0
[113] jsonlite_1.7.2 askpass_1.1 fansi_0.4.2 pillar_1.4.7
[117] lattice_0.20-41 fastmap_1.0.1 httr_1.4.2 GO.db_3.10.0
[121] interactiveDisplayBase_1.24.0 glue_1.4.2 iterators_1.0.13 shinythemes_1.1.2
[125] BiocVersion_3.10.1 bit_4.0.4 ggforce_0.3.2 stringi_1.5.3
[129] blob_1.2.1 caTools_1.18.1 memoise_1.1.0 Got it. Thanks a lot.
run
ah <- AnnotationHub()error
filter() is deprecated as of dplyr 0.7.0 Error in UseMethod("filter") : no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"