* using log directory ‘/srv/hornik/tmp/CRAN/MiscMetabar.Rcheck’
* using R Under development (unstable) (2024-04-22 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘MiscMetabar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MiscMetabar’ version ‘0.8.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/8s] NOTE
Maintainer: ‘Adrien Taudière <adrien.taudiere@zaclys.net>’

Found the following (possibly) invalid URLs:
  URL: \doi{doi:10.1016/10.5061/dryad.tn8qs35}
    From: man/normalize_prop_pq.Rd
    Message: Invalid URI scheme
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MiscMetabar’ can be installed ... [25s/25s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [35s/35s] OK
* checking Rd files ... [1s/1s] WARNING
checkRd: (7) normalize_prop_pq.Rd:29: Invalid URL: \doi{doi:10.1016/10.5061/dryad.tn8qs35}
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [4s/4s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formattable_pq
> ### Title: Create an visualization table to describe taxa distribution
> ###   across a modality
> ### Aliases: formattable_pq
> 
> ### ** Examples
> 
> if (requireNamespace("formattable")) {
+   ## Distribution of the nb of sequences per OTU across Height
+   ##   modality (nb of sequences are log-transformed).
+   ## Only OTU with more than 10000 sequences are taking into account
+   ## The Phylum column is discarded
+   formattable_pq(
+     data_fungi,
+     "Height",
+     min_nb_seq_taxa = 10000,
+     formattable_args = list("Phylum" = FALSE),
+     log10trans = TRUE
+   )
+ 
+   ## Distribution of the nb of samples per OTU across Height modality
+   ## Only OTU  present in more than 50 samples are taking into account
+   formattable_pq(
+     as_binary_otu_table(data_fungi),
+     "Height",
+     min_nb_seq_taxa = 50,
+     formattable_args = list("nb_seq" = FALSE),
+   )
+ 
+   ## Distribution of the nb of sequences per OTU across Time modality
+   ##  arranged by Family Name in ascending order.
+   ## Only OTU with more than 10000 sequences are taking into account
+   ## The Phylum column is discarded
+   formattable_pq(
+     data_fungi,
+     "Time",
+     min_nb_seq_taxa = 10000,
+     taxonomic_levels = c("Order", "Family", "Genus", "Species"),
+     formattable_args = list(
+       Order = FALSE,
+       Species = formattable::formatter(
+         "span",
+         style = x ~ style(
+           "font-style" = "italic",
+           `color` = ifelse(is.na(x), "white", "grey")
+         )
+       )
+     ),
+     arrange_by = "Family",
+     descending_order = FALSE
+   )
+ 
+   ## Distribution of the nb of sequences per OTU across Height modality
+   ##  (nb of sequences are log-transformed).
+   ## OTU name background is light gray for Basidiomycota
+   ##  and dark grey otherwise (Ascomycota)
+   ## A different color is defined for each modality level
+   formattable_pq(
+     data_fungi,
+     "Height",
+     taxonomic_levels = c("Phylum", "Family", "Genus"),
+     void_style = TRUE,
+     formattable_args = list(
+       OTU = formattable::formatter(
+         "span",
+         style = ~ style(
+           "display" = "block",
+           `border-radius` = "5px",
+           `background-color` = ifelse(Phylum == "Basidiomycota", transp("gray"), "gray")
+         ),
+         `padding-right` = "2px"
+       ),
+       High = formattable::formatter(
+         "span",
+         style = x ~ style(
+           "font-size" = "80%",
+           "display" = "inline-block",
+           direction = "rtl",
+           `border-radius` = "0px",
+           `padding-right` = "2px",
+           `background-color` = csscolor(gradient(
+             as.numeric(x), transp("#1a91ff"), "#1a91ff"
+           )),
+           width = percent(proportion(as.numeric(x), na.rm = TRUE))
+         )
+       ),
+       Low = formattable::formatter(
+         "span",
+         style = x ~ style(
+           "font-size" = "80%",
+           "display" = "inline-block",
+           direction = "rtl",
+           `border-radius` = "0px",
+           `padding-right` = "2px",
+           `background-color` = csscolor(gradient(as.numeric(x), transp("green"), "green")),
+           width = percent(proportion(as.numeric(x), na.rm = TRUE))
+         )
+       ),
+       Middle = formattable::formatter(
+         "span",
+         style = x ~ style(
+           "font-size" = "80%",
+           "display" = "inline-block",
+           direction = "rtl",
+           `border-radius` = "0px",
+           `padding-right` = "2px",
+           `background-color` = csscolor(gradient(
+             as.numeric(x), transp("orange"), "orange"
+           )),
+           width = percent(proportion(as.numeric(x), na.rm = TRUE))
+         )
+       )
+     )
+   )
+ }
Loading required namespace: formattable
54 samples were discarded due to NA in variable modality
Cleaning suppress 0 taxa (  ) and 22 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / BG7-010-H_S31_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / D9-027-B_S83_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DJ2-008-H_S88_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / J18-004-B_S114_MERGED.fastq.gz / J18-004-H_S115_MERGED.fastq.gz / J18-004-M_S116_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-H_S166_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
Number of non-matching ASV 0
Number of matching ASV 1420
Number of filtered-out ASV 1400
Number of kept ASV 20
Number of kept samples 109
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
54 samples were discarded due to NA in variable modality
Cleaning suppress 0 taxa (  ) and 35 sample(s) ( B18-006-B_S19_MERGED.fastq.gz / BE9-006-B_S27_MERGED.fastq.gz / BE9-006-H_S28_MERGED.fastq.gz / BE9-006-M_S29_MERGED.fastq.gz / BG7-010-B_S30_MERGED.fastq.gz / BG7-010-H_S31_MERGED.fastq.gz / BL7-006-B_S36_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / CB8-019-B_S69_MERGED.fastq.gz / CB8-019-H_S70_MERGED.fastq.gz / CB8-019-M_S71_MERGED.fastq.gz / D9-027-B_S83_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DJ2-008-H_S88_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / J18-004-B_S114_MERGED.fastq.gz / J18-004-H_S115_MERGED.fastq.gz / J18-004-M_S116_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / N23-002-M_S132_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-B_S158_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / T28-ABM602-B_S162_MERGED.fastq.gz / W26-001-H_S166_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / W9-025-M_S169_MERGED.fastq.gz / Y29-007-B_S181_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
Number of non-matching ASV 0
Number of matching ASV 1420
Number of filtered-out ASV 1417
Number of kept ASV 3
Number of kept samples 96
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
23 samples were discarded due to NA in variable modality
Cleaning suppress 0 taxa (  ) and 14 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
Number of non-matching ASV 0
Number of matching ASV 1420
Number of filtered-out ASV 1390
Number of kept ASV 30
Number of kept samples 148
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
54 samples were discarded due to NA in variable modality
Cleaning suppress 0 taxa (  ) and 5 sample(s) ( DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
Number of non-matching ASV 0
Number of matching ASV 1420
Number of filtered-out ASV 1265
Number of kept ASV 155
Number of kept samples 126
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
Error in style(display = "block", `border-radius` = "5px", `background-color` = ifelse(Phylum ==  : 
  could not find function "style"
Calls: <Anonymous> ... render_html_matrix.data.frame -> f -> lapply -> FUN -> eval_formula -> eval -> eval
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [62s/34s] OK
  Running ‘testthat.R’ [62s/34s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/11s] OK
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE