cmd4: `curatedMetagenomicData` function prints a huge list of species to the console when `dryrun = FALSE`

[lwaldron]

Description

When calling curatedMetagenomicData with dryrun = FALSE and rownames = "short", the function prints a massive list of taxa (over 1,800 lines) directly to the console instead of executing silently. This occurs when it checks for and drops taxa without taxonomy information.

Reproducible Example

library(curatedMetagenomicData)

# cMD version: 4.0.1
packageVersion("curatedMetagenomicData")
#> [1] ‘4.0.1’

# This command should execute silently, but it floods the console with output
re <- curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE, rownames = "short")

Example Output

dropping rows without taxonomy info:
$`AsnicarF_2017.relative_abundance`
  k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii
  k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB346
  k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera_stadtmanae
  k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera_stadtmanae|t__SGB353
...
  <truncated: ~1,800 additional lines>
...
  k__Eukaryota|p__Eukaryota_unclassified|c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis|s__Blastocystis_sp_subtype_1|t__EUK944036

Expected Behavior

The curatedMetagenomicData function should execute without flooding the console. When it drops rows, it should output a concise message.

Recommended Fix

In R/cmd4.R (around line 267), the msg construction uses paste0 with collapse = "\n", which dumps the entire drop_rows vector to the screen:

            msg <- paste0(
                msg, paste0("  ", drop_rows, collapse = "\n"), "\n"
            )

The recommended fix is to either truncate this list (e.g., printing only the first 5 elements followed by "... and N more") or simply print the count of dropped rows.

Example fix using truncation:

            max_print <- 5
            to_print <- head(drop_rows, max_print)
            msg <- paste0(msg, paste0("  ", to_print, collapse = "\n"))
            if (length(drop_rows) > max_print) {
                msg <- paste0(msg, "\n  ... and ", length(drop_rows) - max_print, " more")
            }
            msg <- paste0(msg, "\n")