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AUCell: score single cells with gene regulatory networks
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R 4.3_Error in .read_block_OLD(x, viewport, as.sparse = as.sparse) : could not find function ".read_block_OLD" #39

Closed ClemenceHnn closed 1 year ago

ClemenceHnn commented 1 year ago

Hi aertslab team,

After updating R to 4.3, I get this error message while attempting to run AUCell_run.

Creating expmat dgCMatrix expression matrix from seurat.object, and calculating AUC for the genelist using AUCell_run function:

expmat <- GetAssayData(seurat.object, slot = "counts")
foo <- AUCell::AUCell_run(expmat, genelist)

Error is as following:

Error in .read_block_OLD(x, viewport, as.sparse = as.sparse) : 
  could not find function ".read_block_OLD"

Session info:

session_info()
─ Session info ────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       macOS Ventura 13.2.1
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Paris
 date     2023-05-20
 rstudio  2023.03.1+446 Cherry Blossom (desktop)
 pandoc   2.14.0.3 @ /usr/local/bin/pandoc

─ Packages ────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-5     2016-07-21 [1] CRAN (R 4.3.0)
 annotate               1.78.0    2023-05-11 [1] Bioconductor
 AnnotationDbi          1.62.1    2023-05-11 [1] Bioconductor
 AUCell                 1.22.0    2023-05-11 [1] Bioconductor
 Biobase              * 2.60.0    2023-05-11 [1] Bioconductor
 BiocGenerics         * 0.46.0    2023-05-11 [1] Bioconductor
 BiocManager          * 1.30.20   2023-02-24 [1] CRAN (R 4.3.0)
 Biostrings             2.68.1    2023-05-16 [1] Bioconductor
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.3.0)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.3.0)
 bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.3.0)
 cachem                 1.0.8     2023-05-01 [1] CRAN (R 4.3.0)
 callr                  3.7.3     2022-11-02 [1] CRAN (R 4.3.0)
 cli                    3.6.1     2023-03-23 [1] CRAN (R 4.3.0)
 cluster                2.1.4     2022-08-22 [1] CRAN (R 4.3.0)
 codetools              0.2-19    2023-02-01 [1] CRAN (R 4.3.0)
 colorspace             2.1-0     2023-01-23 [1] CRAN (R 4.3.0)
 cowplot                1.1.1     2020-12-30 [1] CRAN (R 4.3.0)
 crayon                 1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
 data.table             1.14.8    2023-02-17 [1] CRAN (R 4.3.0)
 DBI                    1.1.3     2022-06-18 [1] CRAN (R 4.3.0)
 DelayedArray           0.26.2    2023-05-11 [1] Bioconductor
 DelayedMatrixStats     1.22.0    2023-05-11 [1] Bioconductor
 deldir                 1.0-9     2023-05-17 [1] CRAN (R 4.3.0)
 devtools             * 2.4.5     2022-10-11 [1] CRAN (R 4.3.0)
 digest                 0.6.31    2022-12-11 [1] CRAN (R 4.3.0)
 dplyr                * 1.1.2     2023-04-20 [1] CRAN (R 4.3.0)
 ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.3.0)
 fansi                  1.0.4     2023-01-22 [1] CRAN (R 4.3.0)
 fastmap                1.1.1     2023-02-24 [1] CRAN (R 4.3.0)
 fitdistrplus           1.1-11    2023-04-25 [1] CRAN (R 4.3.0)
 fs                     1.6.2     2023-04-25 [1] CRAN (R 4.3.0)
 future                 1.32.0    2023-03-07 [1] CRAN (R 4.3.0)
 future.apply           1.10.0    2022-11-05 [1] CRAN (R 4.3.0)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.3.0)
 GenomeInfoDb         * 1.36.0    2023-05-11 [1] Bioconductor
 GenomeInfoDbData       1.2.10    2023-05-20 [1] Bioconductor
 GenomicRanges        * 1.52.0    2023-05-11 [1] Bioconductor
 ggplot2                3.4.2     2023-04-03 [1] CRAN (R 4.3.0)
 ggrepel                0.9.3     2023-02-03 [1] CRAN (R 4.3.0)
 ggridges               0.5.4     2022-09-26 [1] CRAN (R 4.3.0)
 globals                0.16.2    2022-11-21 [1] CRAN (R 4.3.0)
 glue                   1.6.2     2022-02-24 [1] CRAN (R 4.3.0)
 goftest                1.2-3     2021-10-07 [1] CRAN (R 4.3.0)
 graph                  1.78.0    2023-05-11 [1] Bioconductor
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.3.0)
 GSEABase               1.62.0    2023-05-11 [1] Bioconductor
 gtable                 0.3.3     2023-03-21 [1] CRAN (R 4.3.0)
 htmltools              0.5.5     2023-03-23 [1] CRAN (R 4.3.0)
 htmlwidgets            1.6.2     2023-03-17 [1] CRAN (R 4.3.0)
 httpuv                 1.6.11    2023-05-11 [1] CRAN (R 4.3.0)
 httr                   1.4.6     2023-05-08 [1] CRAN (R 4.3.0)
 ica                    1.0-3     2022-07-08 [1] CRAN (R 4.3.0)
 igraph                 1.4.2     2023-04-07 [1] CRAN (R 4.3.0)
 IRanges              * 2.34.0    2023-05-11 [1] Bioconductor
 irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.3.0)
 jsonlite               1.8.4     2022-12-06 [1] CRAN (R 4.3.0)
 KEGGREST               1.40.0    2023-05-11 [1] Bioconductor
 KernSmooth             2.23-21   2023-05-03 [1] CRAN (R 4.3.0)
 later                  1.3.1     2023-05-02 [1] CRAN (R 4.3.0)
 lattice                0.21-8    2023-04-05 [1] CRAN (R 4.3.0)
 lazyeval               0.2.2     2019-03-15 [1] CRAN (R 4.3.0)
 leiden                 0.4.3     2022-09-10 [1] CRAN (R 4.3.0)
 lifecycle              1.0.3     2022-10-07 [1] CRAN (R 4.3.0)
 listenv                0.9.0     2022-12-16 [1] CRAN (R 4.3.0)
 lmtest                 0.9-40    2022-03-21 [1] CRAN (R 4.3.0)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.3.0)
 MASS                   7.3-60    2023-05-04 [1] CRAN (R 4.3.0)
 Matrix               * 1.5-4.1   2023-05-18 [1] CRAN (R 4.3.0)
 MatrixGenerics       * 1.12.0    2023-05-11 [1] Bioconductor
 matrixStats          * 0.63.0    2022-11-18 [1] CRAN (R 4.3.0)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.3.0)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.3.0)
 miniUI                 0.1.1.1   2018-05-18 [1] CRAN (R 4.3.0)
 munsell                0.5.0     2018-06-12 [1] CRAN (R 4.3.0)
 nlme                   3.1-162   2023-01-31 [1] CRAN (R 4.3.0)
 parallelly             1.35.0    2023-03-23 [1] CRAN (R 4.3.0)
 patchwork              1.1.2     2022-08-19 [1] CRAN (R 4.3.0)
 pbapply                1.7-0     2023-01-13 [1] CRAN (R 4.3.0)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild               1.4.0     2022-11-27 [1] CRAN (R 4.3.0)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.3.0)
 pkgload                1.3.2     2022-11-16 [1] CRAN (R 4.3.0)
 plotly                 4.10.1    2022-11-07 [1] CRAN (R 4.3.0)
 plyr                   1.8.8     2022-11-11 [1] CRAN (R 4.3.0)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.3.0)
 polyclip               1.10-4    2022-10-20 [1] CRAN (R 4.3.0)
 prettyunits            1.1.1     2020-01-24 [1] CRAN (R 4.3.0)
 processx               3.8.1     2023-04-18 [1] CRAN (R 4.3.0)
 profvis                0.3.8     2023-05-02 [1] CRAN (R 4.3.0)
 progressr              0.13.0    2023-01-10 [1] CRAN (R 4.3.0)
 promises               1.2.0.1   2021-02-11 [1] CRAN (R 4.3.0)
 ps                     1.7.5     2023-04-18 [1] CRAN (R 4.3.0)
 purrr                  1.0.1     2023-01-10 [1] CRAN (R 4.3.0)
 R.methodsS3            1.8.2     2022-06-13 [1] CRAN (R 4.3.0)
 R.oo                   1.25.0    2022-06-12 [1] CRAN (R 4.3.0)
 R.utils                2.12.2    2022-11-11 [1] CRAN (R 4.3.0)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.3.0)
 RANN                   2.6.1     2019-01-08 [1] CRAN (R 4.3.0)
 RColorBrewer           1.1-3     2022-04-03 [1] CRAN (R 4.3.0)
 Rcpp                   1.0.10    2023-01-22 [1] CRAN (R 4.3.0)
 RcppAnnoy              0.0.20    2022-10-27 [1] CRAN (R 4.3.0)
 RCurl                  1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
 remotes                2.4.2     2021-11-30 [1] CRAN (R 4.3.0)
 reshape2               1.4.4     2020-04-09 [1] CRAN (R 4.3.0)
 reticulate             1.28      2023-01-27 [1] CRAN (R 4.3.0)
 rlang                  1.1.1     2023-04-28 [1] CRAN (R 4.3.0)
 ROCR                   1.0-11    2020-05-02 [1] CRAN (R 4.3.0)
 RSQLite                2.3.1     2023-04-03 [1] CRAN (R 4.3.0)
 Rtsne                  0.16      2022-04-17 [1] CRAN (R 4.3.0)
 S4Arrays               1.0.4     2023-05-14 [1] Bioconductor
 S4Vectors            * 0.38.1    2023-05-11 [1] Bioconductor
 scales                 1.2.1     2022-08-20 [1] CRAN (R 4.3.0)
 scattermore            1.1       2023-05-17 [1] CRAN (R 4.3.0)
 sctransform            0.3.5     2022-09-21 [1] CRAN (R 4.3.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.3.0)
 Seurat               * 4.3.0     2022-11-18 [1] CRAN (R 4.3.0)
 SeuratObject         * 4.1.3     2022-11-07 [1] CRAN (R 4.3.0)
 shiny                  1.7.4     2022-12-15 [1] CRAN (R 4.3.0)
 SingleCellExperiment * 1.22.0    2023-05-11 [1] Bioconductor
 sp                     1.6-0     2023-01-19 [1] CRAN (R 4.3.0)
 sparseMatrixStats      1.12.0    2023-05-11 [1] Bioconductor
 spatstat.data          3.0-1     2023-03-12 [1] CRAN (R 4.3.0)
 spatstat.explore       3.2-1     2023-05-13 [1] CRAN (R 4.3.0)
 spatstat.geom          3.2-1     2023-05-09 [1] CRAN (R 4.3.0)
 spatstat.random        3.1-5     2023-05-11 [1] CRAN (R 4.3.0)
 spatstat.sparse        3.0-1     2023-03-12 [1] CRAN (R 4.3.0)
 spatstat.utils         3.0-3     2023-05-09 [1] CRAN (R 4.3.0)
 stringi                1.7.12    2023-01-11 [1] CRAN (R 4.3.0)
 stringr                1.5.0     2022-12-02 [1] CRAN (R 4.3.0)
 SummarizedExperiment * 1.30.1    2023-05-11 [1] Bioconductor
 survival               3.5-5     2023-03-12 [1] CRAN (R 4.3.0)
 tensor                 1.5       2012-05-05 [1] CRAN (R 4.3.0)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.3.0)
 tidyr                  1.3.0     2023-01-24 [1] CRAN (R 4.3.0)
 tidyselect             1.2.0     2022-10-10 [1] CRAN (R 4.3.0)
 urlchecker             1.0.1     2021-11-30 [1] CRAN (R 4.3.0)
 usethis              * 2.1.6     2022-05-25 [1] CRAN (R 4.3.0)
 utf8                   1.2.3     2023-01-31 [1] CRAN (R 4.3.0)
 uwot                   0.1.14    2022-08-22 [1] CRAN (R 4.3.0)
 vctrs                  0.6.2     2023-04-19 [1] CRAN (R 4.3.0)
 viridisLite            0.4.2     2023-05-02 [1] CRAN (R 4.3.0)
 XML                    3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.3.0)
 XVector                0.40.0    2023-05-11 [1] Bioconductor
 zlibbioc               1.46.0    2023-05-11 [1] Bioconductor
 zoo                    1.8-12    2023-04-13 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library

────────────────────────────────────────────────────────────

Would you know how to fix this ?

Thank you very much for your help

cyli0421 commented 1 year ago

I want to know how you solve it. I have the same problem when I use CAGEr.

ClemenceHnn commented 1 year ago

Update to AUCell 1.23 solved the issue. It might also be a package compatibility problem for CAGEr.

Allen1Z commented 1 year ago

Update to AUCell 1.23 solved the issue. It might also be a package compatibility problem for CAGEr.

where can I get AUCell 1.23? I tried to find it in bioconductor,but I only found the version of 1.22