===============================
BiocCheckGitClone('MetaProViz')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz
→ BiocVersion: 3.22
→ Package: MetaProViz
→ PackageVersion: 3.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• MetaProViz.Rproj
* 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...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘3.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 37 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 ... NOTE
unable to verify current time
* 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘SummarizedExperiment’ ‘cosmosR’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘count_id’ ‘viz_upset’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [28s/29s] NOTE
dma_stat_limma: warning in topTable(fit2, coef = contrast_name, n =
Inf, sort.by = "n", adjust.method = padj): partial argument match of
'n' to 'number'
save_res: warning in ggsave(filename = paste0(file_name_Save, ".",
save_plot, sep = ""), plot = inputlist_plot[[Plot]], width =
plot_width, height = plot_height, unit = plot_unit): partial argument
match of 'unit' to 'units'
add_info: no visible global function definition for ‘aggregate’
add_info: no visible binding for global variable ‘targets_detected_num’
add_info: no visible global function definition for ‘desc’
add_info: no visible binding for global variable ‘score’
bartlett: no visible binding for global variable ‘..density..’
check_param_mca: no visible global function definition for
‘complete.cases’
checkmatch_pk_to_data: no visible binding for global variable ‘.data’
checkmatch_pk_to_data: no visible global function definition for
‘everything’
checkmatch_pk_to_data : create_long_df: no visible binding for global
variable ‘row_id’
checkmatch_pk_to_data: no visible binding for global variable
‘OriginalGroup_data’
checkmatch_pk_to_data: no visible binding for global variable
‘OriginalGroup_PK’
checkmatch_pk_to_data: no visible binding for global variable ‘matches’
checkmatch_pk_to_data: no visible binding for global variable
‘Count_FeatureIDs_to_GroupingVariable’
checkmatch_pk_to_data: no visible binding for global variable
‘Group_Conflict_Notes’
checkmatch_pk_to_data: no visible binding for global variable
‘matches_count’
checkmatch_pk_to_data: no visible binding for global variable
‘ActionRequired’
cluster_ora: no visible global function definition for ‘aggregate’
cluster_ora: no visible binding for global variable ‘Description’
cluster_ora: no visible binding for global variable ‘term’
cluster_ora: no visible binding for global variable
‘Metabolites_in_Pathway’
cluster_pk: no visible global function definition for ‘cor’
cluster_pk: no visible binding for global variable ‘Overlap’
cluster_pk: no visible binding for global variable ‘Term1’
cluster_pk: no visible binding for global variable ‘Term2’
cluster_pk: no visible global function definition for ‘hclust’
cluster_pk: no visible global function definition for ‘as.dist’
cluster_pk: no visible binding for global variable ‘distance_matrix’
cluster_pk: no visible global function definition for ‘cutree’
cluster_pk: no visible binding for global variable ‘cluster’
compare_pk : <anonymous>: no visible global function definition for
‘na.omit’
compare_pk: no visible global function definition for ‘na.omit’
compare_pk: no visible binding for global variable ‘Type’
core_norm: no visible global function definition for ‘dev.new’
core_norm: no visible binding for global variable ‘Sample_type’
core_norm: no visible global function definition for ‘dev.off’
core_norm : <anonymous>: no visible global function definition for ‘sd’
core_norm: no visible binding for global variable ‘CV’
core_norm: no visible binding for global variable ‘density’
core_norm: no visible binding for global variable ‘HighVar’
core_norm: no visible global function definition for ‘fisher.test’
core_norm: no visible global function definition for ‘var’
count_id: no visible binding for global variable ‘.data’
count_id: no visible binding for global variable ‘entry_count’
count_id: no visible binding for global variable ‘id_label’
dma : <anonymous>: no visible binding for global variable ‘Metabolite’
dma: no visible global function definition for ‘dev.new’
dma: no visible global function definition for ‘dev.off’
dma_stat_limma: no visible global function definition for
‘model.matrix’
dma_stat_limma: no visible binding for global variable ‘New’
equivalent_id: no visible binding for global variable
‘equivalent_features’
equivalent_id: no visible binding for global variable ‘InputID’
equivalent_id: no visible binding for global variable ‘AdditionalID’
equivalent_id: no visible binding for global variable ‘fromList’
equivalent_id: no visible binding for global variable
‘PotentialAdditionalIDs’
equivalent_id: no visible global function definition for ‘na.omit’
equivalent_id: no visible binding for global variable ‘AllIDs.x’
equivalent_id: no visible binding for global variable ‘AllIDs.y’
equivalent_id: no visible binding for global variable ‘AllIDs’
kruskal: no visible global function definition for ‘everything’
log2fc: no visible binding for global variable ‘Log2(Distance)’
log2fc: no visible binding for global variable ‘C1_Adapted’
log2fc: no visible binding for global variable ‘C2_Adapted’
make_gene_metab_set: no visible global function definition for ‘data’
make_gene_metab_set: no visible binding for global variable ‘feature’
mapping_ambiguity: no visible binding for global variable ‘UniqueID’
mca_2cond: no visible global function definition for ‘complete.cases’
mca_2cond: no visible binding for global variable ‘Cond1_DF_Detected’
mca_2cond: no visible binding for global variable ‘Cond1_DF_Cutoff’
mca_2cond: no visible binding for global variable ‘Cond2_DF_Detected’
mca_2cond: no visible binding for global variable ‘Cond2_DF_Cutoff’
mca_2cond: no visible binding for global variable
‘Cond2_DF_Cutoff_Specific’
mca_2cond: no visible binding for global variable ‘BG_method’
mca_2cond: no visible binding for global variable ‘RG1_All’
mca_2cond: no visible binding for global variable ‘RG2_Significant’
mca_2cond: no visible binding for global variable
‘RG3_SignificantChange’
mca_core: no visible global function definition for ‘complete.cases’
mca_core: no visible binding for global variable ‘Intra_DF_Detected’
mca_core: no visible binding for global variable ‘Intra_DF_Cutoff’
mca_core: no visible binding for global variable ‘core_DF_Detected’
mca_core: no visible binding for global variable ‘core_DF_Cutoff’
mca_core: no visible binding for global variable
‘core_DF_Cutoff_Specific’
mca_core: no visible binding for global variable ‘BG_method’
mca_core: no visible binding for global variable ‘RG1_All’
mca_core: no visible binding for global variable ‘RG2_Significant’
mca_core: no visible binding for global variable ‘RG3_Change’
meta_pk: no visible binding for global variable ‘SampleID’
metadata_analysis: no visible binding for global variable ‘term’
metadata_analysis: no visible binding for global variable ‘PC’
metadata_analysis : <anonymous>: no visible global function definition
for ‘desc’
metadata_analysis: no visible global function definition for
‘everything’
metadata_analysis: no visible binding for global variable
‘tukeyHSD_p.adjusted’
metadata_analysis: no visible binding for global variable ‘feature’
metadata_analysis: no visible binding for global variable
‘Explained_Variance’
metadata_analysis: no visible binding for global variable
‘Sum(Explained_Variance)’
metadata_analysis: no visible binding for global variable ‘MainDriver’
metadata_analysis: no visible global function definition for ‘desc’
metadata_analysis: no visible binding for global variable
‘MainDriver_Sum(VarianceExplained)’
metaproviz_init: no visible binding for global variable ‘OmnipathR’
metaproviz_init: no visible binding for global variable ‘init_config’
metaproviz_init: no visible binding for global variable ‘init_log’
metaproviz_init: no visible binding for global variable
‘.on_buildserver’
metsigdb_chemicalclass: no visible binding for global variable
‘class_source_id’
metsigdb_chemicalclass: no visible binding for global variable
‘chem_source_id’
metsigdb_chemicalclass: no visible binding for global variable
‘class_level_name’
metsigdb_chemicalclass: no visible binding for global variable
‘class_name’
metsigdb_chemicalclass: no visible binding for global variable
‘common_name’
metsigdb_chemicalclass: no visible binding for global variable
‘ClassyFire_class’
metsigdb_chemicalclass: no visible binding for global variable
‘ClassyFire_super_class’
metsigdb_chemicalclass: no visible binding for global variable
‘ClassyFire_sub_class’
metsigdb_kegg: no visible global function definition for ‘everything’
metsigdb_kegg: no visible binding for global variable ‘name.x’
metsigdb_kegg: no visible binding for global variable ‘name.y’
metsigdb_kegg: no visible binding for global variable ‘id_a’
metsigdb_kegg: no visible binding for global variable ‘compound_name’
metsigdb_kegg: no visible binding for global variable ‘compound_names’
metsigdb_kegg: no visible binding for global variable ‘pathway_name’
metsigdb_kegg: no visible binding for global variable ‘compound’
metsigdb_kegg: no visible binding for global variable ‘pathway’
metsigdb_metalinks: no visible binding for global variable
‘protein_type’
metsigdb_metalinks: no visible binding for global variable ‘type’
mvi_imputation: no visible binding for global variable ‘Conditions’
mvi_imputation: no visible global function definition for ‘everything’
mvi_imputation: no visible global function definition for ‘where’
outlier_detection: no visible binding for global variable ‘var’
outlier_detection: no visible global function definition for ‘dev.new’
outlier_detection: no visible global function definition for ‘dev.off’
outlier_detection: no visible binding for global variable ‘Samples’
outlier_detection: no visible binding for global variable ‘Group
summary statisctics’
outlier_detection: no visible binding for global variable ‘Outliers’
outlier_detection: no visible global function definition for ‘relevel’
plot_grob_superplot: no visible binding for global variable
‘Conditions’
pool_estimation : <anonymous>: no visible global function definition
for ‘sd’
pool_estimation: no visible binding for global variable ‘CV’
pool_estimation: no visible global function definition for ‘dev.new’
pool_estimation: no visible binding for global variable ‘Sample_type’
pool_estimation: no visible global function definition for ‘dev.off’
pool_estimation: no visible binding for global variable ‘density’
pool_estimation: no visible binding for global variable ‘HighVar’
replicate_sum: no visible binding for global variable
‘Biological_Replicates’
replicate_sum: no visible binding for global variable ‘Conditions’
replicate_sum: no visible binding for global variable
‘Analytical_Replicates’
replicate_sum: no visible binding for global variable ‘UniqueID’
save_res: no visible global function definition for ‘where’
shapiro : <anonymous>: no visible global function definition for ‘var’
shapiro: no visible global function definition for ‘complete.cases’
shapiro: no visible binding for global variable ‘density’
shapiro: no visible global function definition for ‘plot.new’
shapiro: no visible global function definition for ‘recordPlot’
shapiro: no visible global function definition for ‘dev.off’
standard_ora: no visible binding for global variable
‘Cluster_ChangedMetabolites’
standard_ora: no visible global function definition for ‘aggregate’
standard_ora: no visible binding for global variable ‘Description’
standard_ora: no visible binding for global variable ‘term’
standard_ora: no visible binding for global variable
‘Metabolites_in_Pathway’
tic_norm: no visible binding for global variable ‘median’
tic_norm: no visible global function definition for ‘everything’
tic_norm: no visible global function definition for ‘median’
tic_norm: no visible global function definition for ‘dev.new’
tic_norm: no visible global function definition for ‘dev.off’
viz_pca: no visible global function definition for ‘metaproviz_palette’
viz_stackedbar: no visible binding for global variable ‘total’
viz_superplot: no visible binding for global variable ‘Conditions’
viz_superplot: no visible binding for global variable ‘sd’
viz_superplot: no visible binding for global variable ‘Superplot’
viz_superplot: no visible binding for global variable ‘Intensity’
viz_superplot : data_summary: no visible global function definition for
‘sd’
viz_superplot: no visible binding for global variable ‘comparisons_rev’
viz_upset: no visible binding for global variable ‘upset_plot’
viz_volcano_compare: no visible global function definition for
‘na.omit’
viz_volcano_compare: no visible binding for global variable
‘individual’
viz_volcano_pea: no visible binding for global variable ‘PEA_Pathway’
viz_volcano_pea: no visible binding for global variable ‘PEA_Feature’
viz_volcano_standard: no visible binding for global variable
‘individual’
vst: no visible binding for global variable ‘variable’
vst: no visible binding for global variable ‘value’
vst: no visible global function definition for ‘sd’
vst: no visible binding for global variable ‘sd’
vst: no visible global function definition for ‘coef’
Undefined global functions or variables:
..density.. .data .on_buildserver ActionRequired AdditionalID AllIDs
AllIDs.x AllIDs.y Analytical_Replicates BG_method
Biological_Replicates C1_Adapted C2_Adapted CV ClassyFire_class
ClassyFire_sub_class ClassyFire_super_class
Cluster_ChangedMetabolites Cond1_DF_Cutoff Cond1_DF_Detected
Cond2_DF_Cutoff Cond2_DF_Cutoff_Specific Cond2_DF_Detected Conditions
Count_FeatureIDs_to_GroupingVariable Description Explained_Variance
Group summary statisctics Group_Conflict_Notes HighVar InputID
Intensity Intra_DF_Cutoff Intra_DF_Detected Log2(Distance) MainDriver
MainDriver_Sum(VarianceExplained) Metabolite Metabolites_in_Pathway
New OmnipathR OriginalGroup_PK OriginalGroup_data Outliers Overlap PC
PEA_Feature PEA_Pathway PotentialAdditionalIDs RG1_All
RG2_Significant RG3_Change RG3_SignificantChange SampleID Sample_type
Samples Sum(Explained_Variance) Superplot Term1 Term2 Type UniqueID
aggregate as.dist chem_source_id class_level_name class_name
class_source_id cluster coef common_name comparisons_rev
complete.cases compound compound_name compound_names cor
core_DF_Cutoff core_DF_Cutoff_Specific core_DF_Detected cutree data
density desc dev.new dev.off distance_matrix entry_count
equivalent_features everything feature fisher.test fromList hclust
id_a id_label individual init_config init_log matches matches_count
median metaproviz_palette model.matrix na.omit name.x name.y pathway
pathway_name plot.new protein_type recordPlot relevel row_id score sd
targets_detected_num term total tukeyHSD_p.adjusted type upset_plot
value var variable where
Consider adding
importFrom("base", "summary")
importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
importFrom("graphics", "plot.new")
importFrom("stats", "aggregate", "as.dist", "coef", "complete.cases",
"cor", "cutree", "density", "fisher.test", "hclust",
"median", "model.matrix", "na.omit", "relevel", "sd", "var")
importFrom("utils", "data")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘MetaProViz/R/GetPriorKnowledge.R’:
data("meta_network", package = "cosmosR")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'checkmatch_pk_to_data.Rd':
\examples lines wider than 100 characters:
input_pathway <- translate_id(data= metsigdb_kegg(), metadata_info = c(InputID="MetaboliteID", grouping_variable="term"), from = c("keg ... [TRUNCATED]
Res <- checkmatch_pk_to_data(data= DetectedIDs, input_pk= input_pathway, metadata_info = c(InputID="HMDB", PriorID="hmdb", grouping_var ... [TRUNCATED]
Rd file 'cluster_ora.Rd':
\examples lines wider than 100 characters:
DMAres <- intracell_dma %>% dplyr::filter(!is.na(KEGGCompound))%>%tibble::column_to_rownames("KEGGCompound")%>%dplyr::select(- "Metabol ... [TRUNCATED]
Rd file 'compare_pk.Rd':
\examples lines wider than 100 characters:
# biocrates_features is a data frame with columns: "TrivialName", "CHEBI", "HMDB", "LIMID", and "Class".
Rd file 'mapping_ambiguity.Rd':
\examples lines wider than 100 characters:
InputDF <- translate_id(data= KEGG_Pathways, metadata_info = c(InputID="MetaboliteID", grouping_variable="term"), from = c("kegg"), to ... [TRUNCATED]
Res <- mapping_ambiguity(data= InputDF, from = "MetaboliteID", to = "pubchem", grouping_variable = "term", summary=TRUE)
Rd file 'mca_2cond.Rd':
\examples lines wider than 100 characters:
Input <- MetaProViz::dma(data=Intra[-c(49:58) ,-c(1:3)], metadata_sample=Intra[-c(49:58) , c(1:3)], metadata_info = c(Conditions = "Con ... [TRUNCATED]
Rd file 'mca_core.Rd':
\examples lines wider than 100 characters:
metadata_info = c(Conditions = "Conditions", Biological_Replicates = "Biological_Replicates", core_no ... [TRUNCATED]
metadata_info = c(Conditions = "Conditions", Numerator = NULL, Denominator = "HK2"),
Rd file 'processing.Rd':
\examples lines wider than 100 characters:
metadata_info = c(Conditions = "Conditions", Biological_Replicates = "Biological_Replicates"))
metadata_info = c(Conditions = "Conditions", Biological_Replicates = "Biological_Replicates", core_norm_ ... [TRUNCATED]
Rd file 'replicate_sum.Rd':
\examples lines wider than 100 characters:
metadata_info = c(Conditions="Conditions", Biological_Replicates="Biological_Replicates", Analytical_Re ... [TRUNCATED]
Rd file 'standard_ora.Rd':
\examples lines wider than 100 characters:
DMAres <- intracell_dma %>% dplyr::filter(!is.na(KEGGCompound))%>%tibble::column_to_rownames("KEGGCompound")%>%dplyr::select(- "Metabol ... [TRUNCATED]
Rd file 'translate_id.Rd':
\examples lines wider than 100 characters:
Res <- translate_id(data= KEGG_Pathways, metadata_info = c(InputID="MetaboliteID", grouping_variable="term"), from = c("kegg"), to = c( ... [TRUNCATED]
Rd file 'viz_superplot.Rd':
\examples lines wider than 100 characters:
Res <- viz_superplot(data=Intra[,-c(1:3)], metadata_sample=Intra[,c(1:3)], metadata_info = c(Conditions="Conditions", Superplot = NULL) ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/59s] ERROR
Running examples in ‘MetaProViz-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_pk
> ### Title: Compare Prior Knowledge Resources and/or Columns within a Single
> ### Resource and Generate an UpSet Plot
> ### Aliases: compare_pk
>
> ### ** Examples
>
> ## Example 1: Within-Resource Comparison (Comparing Columns Within a Single data Frame)
>
> # biocrates_features is a data frame with columns: "TrivialName", "CHEBI", "HMDB", "LIMID", and "Class".
> # Here the "Class" column is used as the grouping variable in the UpSet plot.
> data_single <- list(Biocft = biocrates_features)
> metadata_info_single <- list(Biocft = c("CHEBI", "HMDB", "LIMID"))
>
> res_single <- compare_pk(data = data_single, metadata_info = metadata_info_single,
+ plot_name = "Overlap of BioCrates Columns")
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
i Please use tidy evaluation idioms with `aes()`.
i See also `vignette("ggplot2-in-packages")` for more information.
i The deprecated feature was likely used in the MetaProViz package.
Please report the issue at <https://github.com/saezlab/MetaProViz/issues>.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
i Please use `linewidth` instead.
i The deprecated feature was likely used in the ComplexUpset package.
Please report the issue at
<https://github.com/krassowski/complex-upset/issues>.
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
i For the old behavior use `legend.spacing`
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
i For the old behavior use `legend.spacing`
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Error in `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`:
! Can't merge the `axis.text.x` theme element.
Caused by error in `method(merge_element, list(ggplot2::element, class_any))`:
! Only elements of the same class can be merged.
Backtrace:
▆
1. └─MetaProViz::compare_pk(...)
2. └─MetaProViz:::viz_upset(...)
3. └─ComplexUpset::upset(...)
4. └─S7:::Ops.S7_object(...)
5. ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─base_ops[[.Generic]](e1, e2)
10. ├─S7::S7_dispatch()
11. └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
12. └─ggplot2:::add_ggplot(e1, e2, e2name)
13. ├─ggplot2::ggplot_add(object, p, objectname)
14. └─ggplot2:::ggplot_add.default(object, p, objectname)
15. └─ggplot2::update_ggplot(object = object, plot = plot, ...)
16. ├─S7::S7_dispatch()
17. └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(...)
18. ├─S7::set_props(plot, theme = add_theme(plot@theme, object))
19. └─ggplot2:::add_theme(plot@theme, object)
20. ├─rlang::try_fetch(...)
21. │ ├─base::tryCatch(...)
22. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
23. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
24. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
25. │ └─base::withCallingHandlers(...)
26. └─ggplot2::merge_element(t2[[item]], t1[[item]])
27. ├─S7::S7_dispatch()
28. └─ggplot2 (local) `method(merge_element, list(ggplot2::element, class_any))`(new = `<ggpl2::_>`, old = `<elmnt_bl>`, ...)
29. └─cli::cli_abort("Only elements of the same class can be merged.")
30. └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
checkmatch_pk_to_data 42.602 4.502 49.542
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/5s] 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 ... [5s/5s] OK
* DONE
Status: 1 ERROR, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetaProViz_3.99.1.tar.gz')
===============================
── Installing MetaProViz ───────────────────────────────────────────────────────
✔ Package installed successfully
── MetaProViz session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGTJh3U/file382b596417171f/MetaProViz
→ BiocVersion: 3.22
→ Package: MetaProViz
→ PackageVersion: 3.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/9ecbd3367de570e10a69aa4a8c414184eea6bff8/MetaProViz.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpGTJh3U/file382b596417171f/MetaProViz
→ installDir: /tmp/RtmpGTJh3U/file382b597b1213e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaProViz ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 ‘3.99.1’.
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4 to 4.5.0
* 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: Pathways,
Reactome, Clustering
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...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• quick-start.Rmd
* 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...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• DifferentialMetaboliteAnalysis.R (line 752, column 20)
• ...
• VizVolcano.R (line 1154, column 20)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/GetPriorKnowledge.R (line 391, column 11)
• ...
• print() in R/GetPriorKnowledge.R (line 425, column 11)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/HelperChecks.R (line 459, column 16)
• ...
• R/VizSuperplots.R (line 158, column 26)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/DifferentialMetaboliteAnalysis.R (line 199, column 15)
• ...
• R/Processing.R (line 457, column 93)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/DifferentialMetaboliteAnalysis.R (line 221, column 23)
• ...
• R/DifferentialMetaboliteAnalysis.R (line 260, column 33)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 2 times)
• <<- in R/Processing.R (line 950, column 17)
• <<- in R/Processing.R (line 951, column 19)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 78 times)
• suppressWarnings() in R/DifferentialMetaboliteAnalysis.R (line 208, column
15)
• ...
• suppressMessages() in R/VizVolcano.R (line 1229, column 7)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 55
functions greater than 50 lines.
The longest 5 functions are:
• viz_heatmap() (R/VizHeatmap.R): 628 lines
• ...
• dma() (R/DifferentialMetaboliteAnalysis.R): 521 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• metaproviz_load_config.Rd
• ...
• reexports.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• metaproviz_load_config.Rd
• ...
• metaproviz_save_config.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• metaproviz_load_config.Rd
• ...
• metaproviz_save_config.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 2147 lines (12%) are > 80 characters long.
First few lines:
• R/DifferentialMetaboliteAnalysis.R#L238 metadata_sample[ ...
• ...
• vignettes/quick-start.Rmd#L500 For a detailed example of the visualisat ...
i NOTE: Consider 4 spaces instead of tabs; 18 lines (0%) contain tabs.
First few lines:
• R/GetPriorKnowledge.R#L82 return(KEGG_H) ...
• ...
• R/RefactorPriorKnoweldge.R#L2798 } ...
i NOTE: Consider multiples of 4 spaces for line indents; 4524 lines (26%) are
not.
First few lines:
• R/DifferentialMetaboliteAnalysis.R#L178 Subfolder_B <- file.path(folde ...
• ...
• vignettes/quick-start.Rmd#L504 <div class="progress-bar progress-bar- ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 20 NOTES
i See the MetaProViz.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.