Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     OK     skipped     OK  

nebbiolo1 Summary

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Package: chevreulProcess
Version: 0.99.25
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chevreulProcess
BuildTime: 1 minutes 19.52 seconds
CheckCommand: BiocCheckGitClone('chevreulProcess') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3332/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess.install-out.txt chevreulProcess_0.99.25.tar.gz && BiocCheck('chevreulProcess_0.99.25.tar.gz', `new-package`=TRUE)
CheckTime: 6 minutes 19.85 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 4868.73 KiB
BuildID:: chevreulProcess_20250127193147
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: chevreulProcess. 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.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘chevreulProcess/DESCRIPTION’ ... OK
* preparing ‘chevreulProcess’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘chevreulProcess_0.99.25.tar.gz’


nebbiolo1 CHECK output

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 BiocCheckGitClone('chevreulProcess')

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

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess
→ BiocVersion: 3.21
→ Package: chevreulProcess
→ PackageVersion: 0.99.25
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chevreulProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chevreulProcess’ version ‘0.99.25’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘chevreulProcess’ 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 ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [14s/14s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [43s/43s] 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 ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [20s/20s]
 [20s/20s] 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: 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess.Rcheck/00check.log’
for details.





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

 BiocCheck('chevreulProcess_0.99.25.tar.gz')

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

── Installing chevreulProcess ──────────────────────────────────────────────────
✔ Package installed successfully
── chevreulProcess session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpH2A7Qy/file22a562895df73/chevreulProcess
→ BiocVersion: 3.21
→ Package: chevreulProcess
→ PackageVersion: 0.99.25
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/662b5ab1a2552086cbcb19eb8109d78dbab2372f/chevreulProcess.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpH2A7Qy/file22a562895df73/chevreulProcess
→ installDir: /tmp/RtmpH2A7Qy/file22a562475a804f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chevreulProcess ────────────────────────────────────────
* 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...
* Checking R version dependency...
* 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: ImmunoOncology
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 (40%).
* Checking for pinned package versions in DESCRIPTION...
* 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 chevreulProcess...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/wiggleplotr.R (line 55, column 17)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils.R (line 168, column 25)
• R/utils.R (line 169, column 28)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
• sce_de() (R/cluster.R): 68 lines
• record_experiment_data() (R/utils.R): 51 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• integration_workflow.Rd
• ...
• reintegrate_sce.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; 3 lines (0%) are > 80 characters long.
First few lines:
• R/regress_features.R#L18 reg.nocycle <- regressBatches(ob ...
• R/utils.R#L44 metadata(object)[["experiment"]] ...
• R/wiggleplotr.R#L56 "(.bw) do not mat ...
i NOTE: Consider multiples of 4 spaces for line indents; 87 lines (5%) are not.
First few lines:
• R/cluster.R#L22 diffex_scheme ...
• ...
• R/workflow.R#L43 ...
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 v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the chevreulProcess.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo1 BUILD BIN output

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