===============================
R CMD BUILD
===============================
* checking for file ‘Polytect/DESCRIPTION’ ... OK
* preparing ‘Polytect’:
* 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 ‘Polytect_0.99.1.tar.gz’
===============================
BiocCheckGitClone('Polytect')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/5263c6ff892766438502492d694fbfea9df67810/Polytect
→ BiocVersion: 3.20
→ Package: Polytect
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/5263c6ff892766438502492d694fbfea9df67810/Polytect.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/5263c6ff892766438502492d694fbfea9df67810/Polytect
→ 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...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/5263c6ff892766438502492d694fbfea9df67810/Polytect.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘Polytect/DESCRIPTION’ ... OK
* this is package ‘Polytect’ 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 ‘Polytect’ 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 ... [1s/1s] 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 ... [7s/7s] 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
polytect_merge 13.344 2.381 15.729
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[3s/3s] 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('Polytect_0.99.1.tar.gz')
===============================
── Installing Polytect ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Polytect session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwyHMX7/file2307706c1cb7ff/Polytect
→ BiocVersion: 3.20
→ Package: Polytect
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/5263c6ff892766438502492d694fbfea9df67810/Polytect.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpwyHMX7/file2307706c1cb7ff/Polytect
→ installDir: /tmp/RtmpwyHMX7/file230770154c3bce
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Polytect ───────────────────────────────────────────────
* 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...
* 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 (6%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: Installation calls found in vignette(s)
Found in files:
• vignettes/introduction.Rmd (code line 16, column 18)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Polytect...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• polytect_clust.R (line 69, column 40)
• ...
• polytect_merge.R (line 64, column 45)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/internal_functions.R (line 422, column 9)
• print() in R/polytect_clust.R (line 59, column 16)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/polytect_merge.R (line 58, column 15)
• R/polytect_plot.R (line 26, column 14)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/internal_functions.R (line 424, column 21)
• R/internal_functions.R (line 450, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 170 lines (14%) are > 80 characters long.
First few lines:
• R/conc_cal.R#L3 #' This function takes a data frame of f ...
• ...
• vignettes/introduction.Rmd#L194 Lun A (2024). bluster: Clustering Algori ...
i NOTE: Consider multiples of 4 spaces for line indents; 69 lines (6%) are not.
First few lines:
• R/conc_cal.R#L25 ...
• ...
• vignettes/introduction.Rmd#L179 ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 6 NOTES
i See the Polytect.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.