Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/MetaDICT
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     OK     skipped     OK  

nebbiolo2 Summary

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Package: MetaDICT
Version: 0.99.1
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MetaDICT
BuildTime: 7 minutes 13.74 seconds
CheckCommand: BiocCheckGitClone('MetaDICT') && /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3847/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT.install-out.txt MetaDICT_0.99.1.tar.gz && BiocCheck('MetaDICT_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 8 minutes 9.07 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 1007.20 KiB
BuildID:: MetaDICT_20250701202718
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MetaDICT. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘MetaDICT/DESCRIPTION’ ... OK
* preparing ‘MetaDICT’:
* 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
* building ‘MetaDICT_0.99.1.tar.gz’


nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('MetaDICT')

===============================

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT
→ BiocVersion: 3.22
→ Package: MetaDICT
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT
→ 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 for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.7 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/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaDICT/DESCRIPTION’ ... OK
* this is package ‘MetaDICT’ version ‘0.99.1’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetaDICT’ 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] OK
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [381s/381s] OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
metadict_add_new_data 133.492  0.168 133.662
community_detection   119.639  0.289 119.938
metadict              118.351  0.186 118.537
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [12s/12s]
 [12s/12s] 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 ... [3s/3s] OK
* DONE

Status: OK





===============================

 BiocCheck('MetaDICT_0.99.1.tar.gz')

===============================

── Installing MetaDICT ─────────────────────────────────────────────────────────
✔ Package installed successfully
── MetaDICT session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpduMMTA/file22d59e6ed159f5/MetaDICT
→ BiocVersion: 3.22
→ Package: MetaDICT
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3847/d9e078e1bbf546b147ac169796622495442093da/MetaDICT.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpduMMTA/file22d59e6ed159f5/MetaDICT
→ installDir: /tmp/RtmpduMMTA/file22d59e532f9b7e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaDICT ───────────────────────────────────────────────
* 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...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.2.0 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...
* 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 (8%).
* 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• MetaDICT.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MetaDICT...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• data_check.R (line 84, column 19)
• ...
• MetaDICT.R (line 383, column 17)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/MetaDICT_transfer.R (line 190, column 21)
• R/MetaDICT.R (line 191, column 5)
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
• MetaDICT() (R/MetaDICT.R): 146 lines
• ...
• plot_singular_values() (R/singular_val.R): 63 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• data_check.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; 116 lines (8%) are > 80 characters long.
First few lines:
• R/data_check.R#L11 #' @param distance_matrix The distance m ...
• ...
• vignettes/MetaDICT.Rmd#L280 Shared dictionary `D` can be used in tax ...
i NOTE: Consider multiples of 4 spaces for line indents; 158 lines (11%) are
not.
First few lines:
• R/data_check.R#L148 meta_list = meta.list, ...
• ...
• vignettes/MetaDICT.Rmd#L215 customize_param ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the MetaDICT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo2 BUILD BIN output

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