Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/clustSIGNAL
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: clustSIGNAL
Version: 0.99.5
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data clustSIGNAL
BuildTime: 2 minutes 16.04 seconds
CheckCommand: BiocCheckGitClone('clustSIGNAL') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3571/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL.install-out.txt clustSIGNAL_0.99.5.tar.gz && BiocCheck('clustSIGNAL_0.99.5.tar.gz', `new-package`=TRUE)
CheckTime: 7 minutes 7.08 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 4511.25 KiB
BuildID:: clustSIGNAL_20241128010628
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: clustSIGNAL. 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 ‘clustSIGNAL/DESCRIPTION’ ... OK
* preparing ‘clustSIGNAL’:
* 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 ‘clustSIGNAL_0.99.5.tar.gz’


nebbiolo1 CHECK output

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 BiocCheckGitClone('clustSIGNAL')

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

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL
→ BiocVersion: 3.21
→ Package: clustSIGNAL
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL
→ 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

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

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clustSIGNAL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clustSIGNAL’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘clustSIGNAL’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [25s/25s] 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/53s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
adaptiveSmoothing 21.944  0.196  22.144
clustSIGNAL       14.309  0.166  14.477
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [10s/10s]
 [10s/10s] 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('clustSIGNAL_0.99.5.tar.gz')

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

── Installing clustSIGNAL ──────────────────────────────────────────────────────
✔ Package installed successfully
── clustSIGNAL session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8rKibm/file1bd15226f9024d/clustSIGNAL
→ BiocVersion: 3.21
→ Package: clustSIGNAL
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3571/d89f414a7ca07c8ad45a9556a44544d494c4166c/clustSIGNAL.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmp8rKibm/file1bd15226f9024d/clustSIGNAL
→ installDir: /tmp/Rtmp8rKibm/file1bd1522a13de5f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on clustSIGNAL ────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.4.0 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...
i NOTE: Consider adding these automatically suggested biocViews:
ImmunoOncology, DataImport
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 (70%).
* 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 clustSIGNAL...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/entropyMeasure.R (line 46, column 30)
• R/expKernel.R (line 18, column 21)
• R/gaussKernel.R (line 19, column 22)
* 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:
• p1_clustering() (R/initClustering.R): 67 lines
• ...
• clustSIGNAL() (R/clustSIGNAL.R): 54 lines
* Checking man page documentation...
* 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; 41 lines (3%) are > 80 characters long.
First few lines:
• R/adaptiveSmoothing.R#L6 #' are smoothed less with higher weights ...
• ...
• vignettes/clustSIGNAL.Rmd#L349 Clustering and entropy results can be ca ...
i NOTE: Consider multiples of 4 spaces for line indents; 153 lines (11%) are
not.
First few lines:
• R/adaptiveSmoothing.R#L60 f ...
• ...
• vignettes/clustSIGNAL.Rmd#L481 title = "Entropy spread (top) and ...
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 6 NOTES
i See the clustSIGNAL.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo1 BUILD BIN output

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