Column 4 ['rep..TF_lowConf...length.peaks..'] of item 2 is missing in item 1.

[sylestiel]

cisTopicObject<- getCistromes(cisTopicObject, annotation = 'Both', nCores=1)
Column 4 ['rep..TF_lowConf...length.peaks..'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
Column 4 ['rep..TF_lowConf...length.peaks..'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
Column 4 ['rep..TF_lowConf...length.peaks..'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.

This message keeps repeating.....

Suggestions?

Thanks,

[cbravo93]

Hi @sylestiel !

Can you post your sessionInfo()? It may be related to the data.table version.

Cheers!

C

[sylestiel]

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
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] grid parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] rtracklayer_1.46.0 RcisTarget_1.9.1 AUCell_1.9.9
[4] ChIPseeker_1.22.1 fitdistrplus_1.1-1 survival_3.2-3
[7] MASS_7.3-53 ComplexHeatmap_2.2.0 fastcluster_1.1.25
[10] scatterplot3d_0.3-41 plotly_4.9.2.1 ggplot2_3.3.2
[13] umap_0.2.6.0 Matrix_1.2-18 cisTopic_0.3.0
[16] densityClust_0.3 org.Mm.eg.db_3.10.0 TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[19] GenomicFeatures_1.38.2 AnnotationDbi_1.48.0 Biobase_2.46.0
[22] rGREAT_1.18.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[25] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[28] data.table_1.13.0 Rtsne_0.15

loaded via a namespace (and not attached):
[1] reticulate_1.16 R.utils_2.10.1 tidyselect_1.1.0
[4] RSQLite_2.2.0 htmlwidgets_1.5.1 BiocParallel_1.20.1
[7] munsell_0.5.0 codetools_0.2-16 DT_0.15
[10] withr_2.2.0 colorspace_1.4-1 GOSemSim_2.12.1
[13] knitr_1.29 rstudioapi_0.11 DOSE_3.12.0
[16] labeling_0.3 urltools_1.7.3 GenomeInfoDbData_1.2.2
[19] lgr_0.3.4 polyclip_1.10-0 bit64_4.0.5
[22] farver_2.0.3 vctrs_0.3.4 generics_0.0.2
[25] xfun_0.17 float_0.2-4 BiocFileCache_1.10.2
[28] R6_2.4.1 clue_0.3-57 graphlayouts_0.7.0
[31] bitops_1.0-6 fgsea_1.12.0 gridGraphics_0.5-0
[34] DelayedArray_0.12.3 assertthat_0.2.1 promises_1.1.1
[37] scales_1.1.1 ggraph_2.0.3 enrichplot_1.6.1
[40] gtable_0.3.0 tidygraph_1.2.0 rlang_0.4.7
[43] GlobalOptions_0.1.2 text2vec_0.6 splines_3.6.2
[46] lazyeval_0.2.2 europepmc_0.4 BiocManager_1.30.10
[49] yaml_2.2.1 reshape2_1.4.4 crosstalk_1.1.0.1
[52] httpuv_1.5.4 qvalue_2.18.0 tools_3.6.2
[55] feather_0.3.5 ggplotify_0.0.5 ellipsis_0.3.1
[58] gplots_3.0.4 RColorBrewer_1.1-2 ggridges_0.5.2
[61] Rcpp_1.0.5 plyr_1.8.6 progress_1.2.2
[64] zlibbioc_1.32.0 purrr_0.3.4 RCurl_1.98-1.2
[67] prettyunits_1.1.1 openssl_1.4.2 GetoptLong_1.0.2
[70] viridis_0.5.1 cowplot_1.1.0 zoo_1.8-8
[73] SummarizedExperiment_1.16.1 ggrepel_0.8.2 cluster_2.1.0
[76] magrittr_1.5 RSpectra_0.16-0 DO.db_2.9
[79] circlize_0.4.10 triebeard_0.3.0 mlapi_0.1.0
[82] matrixStats_0.56.0 hms_0.5.3 mime_0.9
[85] xtable_1.8-4 RhpcBLASctl_0.20-137 XML_3.99-0.3
[88] gridExtra_2.3 shape_1.4.5 compiler_3.6.2
[91] biomaRt_2.42.1 tibble_3.0.3 KernSmooth_2.23-17
[94] crayon_1.3.4 R.oo_1.24.0 htmltools_0.5.0
[97] later_1.1.0.1 snow_0.4-3 tidyr_1.1.2
[100] DBI_1.1.0 tweenr_1.0.1 dbplyr_1.4.4
[103] rappdirs_0.3.1 boot_1.3-25 gdata_2.18.0
[106] R.methodsS3_1.8.1 igraph_1.2.5 pkgconfig_2.0.3
[109] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 rvcheck_0.1.8 GenomicAlignments_1.22.1
[112] rsparse_0.4.0 xml2_1.3.2 foreach_1.5.0
[115] annotate_1.64.0 lda_1.4.2 XVector_0.26.0
[118] stringr_1.4.0 digest_0.6.25 graph_1.64.0
[121] Biostrings_2.54.0 fastmatch_1.1-0 GSEABase_1.48.0
[124] curl_4.3 shiny_1.5.0 Rsamtools_2.2.3
[127] gtools_3.8.2 rjson_0.2.20 lifecycle_0.2.0
[130] jsonlite_1.7.1 viridisLite_0.3.0 askpass_1.1
[133] pillar_1.4.6 lattice_0.20-41 plotrix_3.7-8
[136] fastmap_1.0.1 httr_1.4.2 GO.db_3.10.0
[139] glue_1.4.2 FNN_1.1.3 png_0.1-7
[142] iterators_1.0.12 bit_4.0.4 ggforce_0.3.2
[145] stringi_1.5.3 blob_1.2.1 caTools_1.18.0
[148] doSNOW_1.0.18 memoise_1.1.0 dplyr_1.0.2

[AAA-3]

I am also getting this error with the melanoma tutorial