===============================
R CMD BUILD
===============================
* checking for file ‘MetaProViz/DESCRIPTION’ ... OK
* preparing ‘MetaProViz’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘MetaProViz/inst/scripts’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘MetaProViz_3.99.14.tar.gz’
===============================
BiocCheckGitClone('MetaProViz')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/MetaProViz
→ BiocVersion: 3.22
→ Package: MetaProViz
→ PackageVersion: 3.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/MetaProViz.BiocCheck
→ BiocCheckVersion: 1.47.0
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/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 v1.47.0 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/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/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 ‘3.99.14’
* 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 ... 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [57s/57s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
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 '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"))
metadata_info = c(Conditions = "Conditions", Biological_Replicates = "Biological_Replicates", core_norm_ ... [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]
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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [465s/465s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mapping_ambiguity 89.740 9.950 99.385
translate_id 68.728 8.494 77.244
processing 65.491 4.752 70.310
metadata_analysis 44.835 4.142 48.888
checkmatch_pk_to_data 31.862 4.014 35.774
mca_core 33.857 2.018 35.882
dma 16.215 1.035 17.243
mca_2cond 6.884 0.489 7.366
pool_estimation 6.411 0.354 6.769
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/14s]
[14s/14s] 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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/MetaProViz.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('MetaProViz_3.99.14.tar.gz')
===============================
── Installing MetaProViz ───────────────────────────────────────────────────────
✔ Package installed successfully
── MetaProViz session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6CwSt5/file25fda919a18a8d/MetaProViz
→ BiocVersion: 3.22
→ Package: MetaProViz
→ PackageVersion: 3.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/1cfb3b14d2ea2d061177eff8ded82be9cdb225a8/MetaProViz.BiocCheck
→ BiocCheckVersion: 1.47.0
→ sourceDir: /tmp/Rtmp6CwSt5/file25fda919a18a8d/MetaProViz
→ installDir: /tmp/Rtmp6CwSt5/file25fda96b1a5381
→ 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 ‘3.99.14’.
* 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: 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 (12%).
* 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 58
functions greater than 50 lines.
The longest 5 functions are:
• viz_heatmap() (R/VizHeatmap.R): 701 lines
• ...
• mapping_ambiguity() (R/RefactorPriorKnoweldge.R): 524 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• compare_pk.Rd
• ...
• reexports.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:
• compare_pk.Rd
• ...
• metaproviz_save_config.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• compare_pk.Rd
• ...
• metaproviz_save_config.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; 2223 lines (12%) are > 80 characters long.
First few lines:
• R/DifferentialMetaboliteAnalysis.R#L219 # ##################################
...
• ...
• 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 v1.47.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 7 NOTES
i See the MetaProViz.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.