===============================
BiocCheckGitClone('MetaProViz')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz
BiocVersion: 3.23
Package: MetaProViz
PackageVersion: 3.99.28
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.1 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MetaProViz/DESCRIPTION ... OK
* checking extension type ... Package
* this is package MetaProViz version 3.99.28
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package MetaProViz can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [12s/12s] 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 ... [60s/60s] NOTE
standard_ora: no visible binding for global variable top/Bottom
Undefined global functions or variables:
top/Bottom
* checking Rd files ... [0s/0s] OK
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [42s/42s] ERROR
Running examples in MetaProViz-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: equivalent_id
> ### Title: Find additional potential IDs for "kegg", "pubchem", "chebi",
> ### "hmdb"
> ### Aliases: equivalent_id
>
> ### ** Examples
>
> data(cellular_meta)
> DetectedIDs <- cellular_meta %>% tidyr::drop_na()
> Res <- equivalent_id(
+ data = DetectedIDs,
+ metadata_info = c(InputID = "HMDB"),
+ from = "hmdb"
+ )
[2025-11-26 12:48:46] [ERROR] [MetaProViz] OmnipathR version: 3.19.2
[2025-11-26 12:48:46] [WARN] [MetaProViz] The following IDs are duplicated and removed: HMDB0000725, HMDB0000267, HMDB0000755
Warning in equivalent_id(data = DetectedIDs, metadata_info = c(InputID = "HMDB"), :
The following IDs are duplicated and removed: HMDB0000725, HMDB0000267, HMDB0000755
chebi is used to find additional potential IDs for hmdb.
Error in `map_int()`:
i In index: 1.
Caused by error in `mutate()`:
i In argument: `latin_name = coalesce(latin_name_uniprot,
latin_name_ensembl, latin_name_oma)`.
Caused by error in `coalesce()`:
! Can't combine `..1` <character> and `..3` <double>.
Backtrace:
1. MetaProViz::equivalent_id(...)
2. ... %>% ...
3. OmnipathR::translate_ids(...)
4. organism %<>% ncbi_taxid
5. dplyr::mutate(., across(all_of(to), ~ifelse(. == "0", NA, .)))
6. dplyr::distinct(.)
7. dplyr::ungroup(.)
8. dplyr::mutate(...)
9. dplyr::group_by(., !!sym(metadata_info[["InputID"]]))
10. dplyr::mutate(...)
11. dplyr::select(., all_of(intersect(names(.), names(data))), all_of(to))
12. OmnipathR::ncbi_taxid(.)
13. name %>% map_int(taxon_name, "ncbi") %>% as.integer
14. purrr::map_int(., taxon_name, "ncbi")
15. purrr:::map_("integer", .x, .f, ..., .progress = .progress)
16. purrr:::with_indexed_errors(...)
17. base::withCallingHandlers(...)
18. purrr:::call_with_cleanup(...)
19. OmnipathR (local) .f(.x[[i]], ...)
20. ... %>% if_null_len0(NA)
21. OmnipathR::get_db("organisms")
22. OmnipathR::load_db(key, param = param)
23. rlang::exec(loader, !!!param)
24. OmnipathR (local) `<fn>`()
25. ... %>% ...
26. OmnipathR:::if_null_len0(., NA)
27. value1 %>% is_empty_2 %>% if (value2) value1
28. OmnipathR:::is_empty_2(.)
29. value %>% ...
30. dplyr::pull(., name_type)
31. dplyr::filter(...)
32. dplyr::mutate(...)
33. dplyr:::mutate.data.frame(...)
34. dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
35. base::withCallingHandlers(...)
36. dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
37. mask$eval_all_mutate(quo)
38. dplyr (local) eval()
39. dplyr::coalesce(latin_name_uniprot, latin_name_ensembl, latin_name_oma)
40. dplyr:::vec_case_when(...)
41. vctrs::vec_ptype_common(!!!everything, .ptype = ptype, .call = call)
42. vctrs (local) `<fn>`()
43. vctrs::vec_default_ptype2(...)
44. base::withRestarts(...)
45. base (local) withOneRestart(expr, restarts[[1L]])
46. base (local) doWithOneRestart(return(expr), restart)
47. vctrs::stop_incompatible_type(...)
48. vctrs:::stop_incompatible(...)
49. vctrs:::stop_vctrs(...)
50. rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dma 15.784 1.26 16.998
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [15s/15s]
[15s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz.Rcheck/00check.log
for details.
===============================
BiocCheck('MetaProViz_3.99.28.tar.gz')
===============================
Installing MetaProViz
Package installed successfully
MetaProViz session metadata
sourceDir: /tmp/RtmpIX36bG/file3bd1ff16836a38/MetaProViz
BiocVersion: 3.23
Package: MetaProViz
PackageVersion: 3.99.28
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/MetaProViz_20251126122234/MetaProViz.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpIX36bG/file3bd1ff16836a38/MetaProViz
installDir: /tmp/RtmpIX36bG/file3bd1ff5badcc77
isTarBall: TRUE
platform: unix
Running BiocCheck on MetaProViz
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got 3.99.28.
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: Reactome
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MetaProViz...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 60
functions greater than 50 lines.
The longest 5 functions are:
mca_core() (R/MetaboliteClusteringAnalysis.R): 1686 lines
...
mapping_ambiguity() (R/RefactorPriorKnoweldge.R): 574 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
checkmatch_pk_to_data.Rd
...
translate_id.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
Found in files:
checkmatch_pk_to_data.Rd
...
translate_id.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
checkmatch_pk_to_data.Rd
...
translate_id.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1259 lines (6%) are > 80 characters long.
First few lines:
R/DifferentialMetaboliteAnalysis.R#L38 #' @param metadata_info Named
character ...
...
vignettes/quick-start.Rmd#L471 For a detailed example of the visualisat ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.1 results
0 ERRORS | 1 WARNINGS | i 7 NOTES
i See the MetaProViz.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.