kableExtra
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Published
20 hours ago •
haozhu233
haozhu233
collapse_rows() not working
Using collapse_rows() does nothing, even with the example code from the manual page:
x <- knitr::kable(dt, "html")
collapse_rows(x)
A colleague of mine was able to get it to work in R version 4.0.2, so I wonder if it's a version issue?
Session info:
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.4 recipes_0.1.15 RedoControl_0.1.1
[4] MASS_7.3-53.1 caret_6.0-86 mblm_0.12.1
[7] ggbeeswarm_0.6.0 rcompanion_2.3.27 phyloseqCompanion_0.2.1
[10] GUniFrac_1.1 matrixStats_0.58.0 doParallel_1.0.16
[13] iterators_1.0.13 foreach_1.5.1 phyloseq_1.32.0
[16] magrittr_2.0.1 gt_0.2.2 broom_0.7.5
[19] RColorBrewer_1.1-2 picante_1.8.2 nlme_3.1-152
[22] vegan_2.5-7 lattice_0.20-41 permute_0.9-5
[25] ape_5.4-1 usedist_0.4.0 cowplot_1.1.1
[28] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5
[31] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[34] tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0
[37] data.table_1.14.0 knitr_1.31
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 Hmisc_4.5-0 systemfonts_1.0.1
[5] plyr_1.8.6 igraph_1.2.6 splines_4.0.4 TH.data_1.0-10
[9] digest_0.6.27 htmltools_0.5.1.1 rsconnect_0.8.16 fansi_0.4.2
[13] checkmate_2.0.0 cluster_2.1.1 Biostrings_2.56.0 modelr_0.1.8
[17] gower_0.2.2 svglite_2.0.0 sandwich_3.0-0 prettyunits_1.1.1
[21] jpeg_0.1-8.1 colorspace_2.0-0 rvest_1.0.0 haven_2.3.1
[25] xfun_0.22 crayon_1.4.1 jsonlite_1.7.2 libcoin_1.0-8
[29] Exact_2.1 survival_3.2-7 zoo_1.8-9 glue_1.4.2
[33] gtable_0.3.0 ipred_0.9-11 zlibbioc_1.34.0 XVector_0.28.0
[37] webshot_0.5.2 Rhdf5lib_1.10.1 BiocGenerics_0.34.0 scales_1.1.1
[41] mvtnorm_1.1-1 DBI_1.1.1 Rcpp_1.0.6 viridisLite_0.3.0
[45] htmlTable_2.1.0 progress_1.2.2 foreign_0.8-81 Formula_1.2-4
[49] stats4_4.0.4 lava_1.6.9 prodlim_2019.11.13 htmlwidgets_1.5.3
[53] httr_1.4.2 ellipsis_0.3.1 modeltools_0.2-23 farver_2.1.0
[57] pkgconfig_2.0.3 sass_0.3.1 nnet_7.3-15 multcompView_0.1-8
[61] dbplyr_2.1.0 utf8_1.1.4 labeling_0.4.2 tidyselect_1.1.0
[65] rlang_0.4.10 reshape2_1.4.4 munsell_0.5.0 cellranger_1.1.0
[69] tools_4.0.4 cli_2.3.1 generics_0.1.0 ade4_1.7-16
[73] evaluate_0.14 EMT_1.1 biomformat_1.16.0 yaml_2.2.1
[77] ModelMetrics_1.2.2.2 fs_1.5.0 fitdistrplus_1.1-3 coin_1.4-1
[81] rootSolve_1.8.2.1 xml2_1.3.2 compiler_4.0.4 rstudioapi_0.13
[85] png_0.1-7 beeswarm_0.3.1 e1071_1.7-4 reprex_1.0.0
[89] statmod_1.4.35 bslib_0.2.4 DescTools_0.99.40 stringi_1.5.3
[93] highr_0.8 Matrix_1.3-2 commonmark_1.7 multtest_2.44.0
[97] vctrs_0.3.6 pillar_1.5.1 lifecycle_1.0.0 BiocManager_1.30.10
[101] jquerylib_0.1.3 lmtest_0.9-38 lmom_2.8 latticeExtra_0.6-29
[105] R6_2.5.0 gridExtra_2.3 vipor_0.4.5 IRanges_2.22.2
[109] gld_2.6.2 codetools_0.2-18 boot_1.3-27 assertthat_0.2.1
[113] rhdf5_2.32.4 nortest_1.0-4 withr_2.4.1 multcomp_1.4-16
[117] S4Vectors_0.26.1 mgcv_1.8-34 expm_0.999-6 hms_1.0.0
[121] grid_4.0.4 rpart_4.1-15 timeDate_3043.102 class_7.3-18
[125] rmarkdown_2.7 pROC_1.17.0.1 base64enc_0.1-3 Biobase_2.48.0
[129] lubridate_1.7.10 tinytex_0.30
@haozhu233 I confirm this is the same problematic behaviour as in #595: collapse_rows() seems to not alter its input. Meanwhile, this issue has been duplicated in #624 as well.
Upon debugging with the example from #624 (which I can reproduce as well), I presume it's because the mapping_matrix dataframe coming out of the internal collapse_row_matrix() function just looks like the following:
> mapping_matrix
x1 x2
1 1 1
Its (presumably wrong?) contents are created here, where the inputs (columns, kable_dt) seem still correct:
https://github.com/haozhu233/kableExtra/blob/a6af5c067c2b4ca8317736f4a3e6c0f7db508fef/R/collapse_rows.R#L145-L148
Session info
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.1.0 (2021-05-18)
os Linux Mint 20
system x86_64, linux-gnu
ui X11
language nl_BE:nl
collate nl_BE.UTF-8
ctype nl_BE.UTF-8
tz Europe/Brussels
date 2021-06-18
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
bslib 0.2.5.1 2021-05-18 [1] CRAN (R 4.1.0)
cli 2.5.0 2021-04-26 [1] CRAN (R 4.1.0)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.1.0)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0)
highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
kableExtra * 1.3.4 2021-02-20 [1] CRAN (R 4.1.0)
knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.1.0)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0)
rmarkdown 2.8 2021-05-07 [1] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
rvest 1.0.0 2021-03-09 [1] CRAN (R 4.1.0)
sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
svglite 2.0.0 2021-02-20 [1] CRAN (R 4.1.0)
systemfonts 1.0.2 2021-05-11 [1] CRAN (R 4.1.0)
tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0)
webshot 0.5.2 2019-11-22 [1] CRAN (R 4.1.0)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
xfun 0.23 2021-05-15 [1] CRAN (R 4.1.0)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0)
[1] /home/floris/lib/R/library
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
As @jacpete comments in https://github.com/haozhu233/kableExtra/issues/595#issuecomment-906646896 and https://github.com/haozhu233/kableExtra/issues/624#issuecomment-906640656, the problem is fixed in the GitHub development version, but not yet on CRAN. This issue seems a duplicate.
I confirm this is working on dev version. Does anybody know if a new CRAN version is planned?
