I am trying to run CHiCdiff with test dataset, however, I got the following error message, could you help me with this? Thank you!
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “DFrame” is not valid for slot ‘elementMetadata’ in an object of class “DESeqResults”; is(value, "DataTable_OR_NULL") is not TRUE
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 (2020-04-24)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-09-04
Hello,
I am trying to run CHiCdiff with test dataset, however, I got the following error message, could you help me with this? Thank you! Error in checkSlotAssignment(object, name, value) : assignment of an object of class “DFrame” is not valid for slot ‘elementMetadata’ in an object of class “DESeqResults”; is(value, "DataTable_OR_NULL") is not TRUE In addition: Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors
─ Packages ─────────────────────────────────────────────────────────────────────────────────────── ! package version date lib annotate 1.66.0 2020-04-27 [2] AnnotationDbi 1.50.3 2020-07-25 [2] assertthat 0.2.1 2019-03-21 [2] VP backports 1.1.8 2020-08-24 [2] base64enc 0.1-3 2015-07-28 [2] Biobase 2.49.0 2020-04-27 [1] BiocGenerics 0.35.4 2020-06-04 [1] BiocParallel 1.23.2 2020-07-06 [1] bit 4.0.4 2020-08-04 [1] bit64 4.0.5 2020-08-30 [1] bitops 1.0-6 2013-08-17 [2] blob 1.2.1 2020-01-20 [2] callr 3.4.3 2020-03-28 [2] checkmate 2.0.0 2020-02-06 [2] Chicago 1.16.0 2020-04-27 [1] Chicdiff 0.6 2020-09-04 [1] ChicdiffData 0.2 2020-09-04 [1] cli 2.0.2 2020-02-28 [2] cluster 2.1.0 2019-06-19 [3] colorspace 1.4-1 2019-03-18 [2] cowplot 1.0.0 2019-07-11 [2] crayon 1.3.4 2017-09-16 [2] curl 4.3 2019-12-02 [2] data.table 1.13.0 2020-07-24 [2] DBI 1.1.0 2019-12-15 [2] Delaporte 7.0.3 2020-06-01 [1] DelayedArray 0.14.1 2020-07-14 [2] desc 1.2.0 2018-05-01 [2] DESeq2 1.28.1 2020-05-12 [2] devtools 2.3.1 2020-07-21 [1] digest 0.6.25 2020-02-23 [2] dplyr 1.0.1 2020-07-31 [2] ellipsis 0.3.1 2020-05-15 [2] fansi 0.4.1 2020-01-08 [2] fdrtool 1.2.15 2015-07-08 [2] FMStable 0.1-2 2012-09-06 [1] foreign 0.8-80 2020-05-24 [3] Formula 1.2-3 2018-05-03 [2] fs 1.5.0 2020-07-31 [2] genefilter 1.70.0 2020-04-27 [2] geneplotter 1.66.0 2020-04-27 [2] generics 0.0.2 2018-11-29 [2] GenomeInfoDb 1.24.2 2020-06-15 [2] GenomeInfoDbData 1.2.3 2020-05-22 [2] GenomicRanges 1.40.0 2020-04-27 [2] ggplot2 3.3.2 2020-06-19 [2] VP glue 1.4.1 2020-08-27 [2] gridExtra 2.3 2017-09-09 [2] gtable 0.3.0 2019-03-25 [2] harmonicmeanp 3.0 2019-08-19 [1] hexbin 1.28.1 2020-02-03 [2] Hmisc 4.4-1 2020-08-10 [2] htmlTable 2.0.1 2020-07-05 [2] htmltools 0.5.0 2020-06-16 [2] htmlwidgets 1.5.1 2019-10-08 [2] IHW 1.17.0 2020-04-27 [1] IRanges 2.23.10 2020-06-13 [1] jpeg 0.1-8.1 2019-10-24 [2] knitr 1.29 2020-06-23 [2] lattice 0.20-41 2020-04-02 [3] latticeExtra 0.6-29 2019-12-19 [2] lifecycle 0.2.0 2020-03-06 [2] locfit 1.5-9.4 2020-03-25 [2] lpsymphony 1.16.0 2020-04-27 [2] magrittr 1.5 2014-11-22 [2] MASS 7.3-51.6 2020-04-26 [3] Matrix 1.2-18 2019-11-27 [3] matrixStats 0.56.0 2020-03-13 [2] memoise 1.1.0 2017-04-21 [2] munsell 0.5.0 2018-06-12 [2] nnet 7.3-14 2020-04-26 [3] pillar 1.4.6 2020-07-10 [1] pkgbuild 1.1.0 2020-07-13 [1] pkgconfig 2.0.3 2019-09-22 [2] pkgload 1.1.0 2020-05-29 [2] png 0.1-7 2013-12-03 [2] prettyunits 1.1.1 2020-01-24 [2] VP processx 3.4.3 2020-09-03 [2] ps 1.3.4 2020-08-11 [2] purrr 0.3.4 2020-04-17 [2] R6 2.4.1 2019-11-12 [2] RColorBrewer 1.1-2 2014-12-07 [2] Rcpp 1.0.5 2020-07-06 [1] RCurl 1.98-1.2 2020-04-18 [2] remotes 2.2.0 2020-07-21 [2] rlang 0.4.7 2020-07-09 [1] rpart 4.1-15 2019-04-12 [3] rprojroot 1.3-2 2018-01-03 [2] RSQLite 2.2.0 2020-01-07 [2] rstudioapi 0.11 2020-02-07 [2] S4Vectors 0.27.12 2020-06-09 [1] scales 1.1.1 2020-05-11 [2] sessioninfo 1.1.1 2018-11-05 [2] slam 0.1-47 2019-12-21 [2] stringi 1.4.6 2020-02-17 [2] stringr 1.4.0 2019-02-10 [2] SummarizedExperiment 1.18.2 2020-07-09 [2] survival 3.2-3 2020-06-13 [3] testthat 2.3.2 2020-03-02 [2] tibble 3.0.3 2020-07-10 [2] tidyselect 1.1.0 2020-05-11 [2] usethis 1.6.1 2020-04-29 [2] vctrs 0.3.4 2020-08-29 [1] withr 2.2.0 2020-04-20 [2] xfun 0.16 2020-07-24 [2] XML 3.99-0.5 2020-07-23 [2] xtable 1.8-4 2019-04-21 [2] XVector 0.28.0 2020-04-27 [2] yaml 2.2.1 2020-02-01 [2] zlibbioc 1.35.0 2020-04-27 [1] source
Bioconductor
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
Bioconductor
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
Github (RegulatoryGenomicsGroup/chicdiff@0aa0820) Github (RegulatoryGenomicsGroup/chicdiff@0aa0820) CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
CRAN (R 4.0.0)
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
Bioconductor
CRAN (R 4.0.0)
Bioconductor
Bioconductor
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
CRAN (R 4.0.0)
Bioconductor
CRAN (R 4.0.0)
Bioconductor
[1] /spin1/home/linux/xieb2/R/4.0/library [2] /usr/local/apps/R/4.0/site-library_4.0.0 [3] /usr/local/apps/R/4.0/4.0.0/lib64/R/library
V ── Loaded and on-disk version mismatch. P ── Loaded and on-disk path mismatch.