===============================
R CMD BUILD
===============================
* checking for file plyxp/DESCRIPTION ... OK
* preparing plyxp:
* 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 plyxp_0.99.21.tar.gz
===============================
BiocCheckGitClone('plyxp')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp
BiocVersion: 3.20
Package: plyxp
PackageVersion: 0.99.21
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp
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 v1.41.17 results
0 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/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp.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 plyxp/DESCRIPTION ... OK
* this is package plyxp version 0.99.21
* 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 plyxp 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking whether startup messages can be suppressed ... [7s/7s] 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 ... [23s/23s] 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 ... WARNING
Codoc mismatches from Rd file 'reexports.Rd':
SummarizedExperiment
Code: function(assays = SimpleList(), rowData = NULL, rowRanges =
NULL, colData = DataFrame(), metadata = list(),
checkDimnames = TRUE)
Docs: function(assays = SimpleList(), rowData = NULL, rowRanges =
GRangesList(), colData = DataFrame(), metadata =
list(), checkDimnames = TRUE)
Mismatches in argument default values:
Name: 'rowRanges' Code: NULL Docs: GRangesList()
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [22s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [11s/11s]
[11s/11s] 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: 1 WARNING
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp.Rcheck/00check.log
for details.
===============================
BiocCheck('plyxp_0.99.21.tar.gz')
===============================
Installing plyxp
Package installed successfully
plyxp session metadata
sourceDir: /tmp/Rtmp1KCYxF/fileb55f8421783b4/plyxp
BiocVersion: 3.20
Package: plyxp
PackageVersion: 0.99.21
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3616/fa261e8fc4ee3e47710a0f183b5d3de309c01bb7/plyxp.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /tmp/Rtmp1KCYxF/fileb55f8421783b4/plyxp
installDir: /tmp/Rtmp1KCYxF/fileb55f854cf4e4a
isTarBall: TRUE
platform: unix
Running BiocCheck on plyxp
* 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...
* 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 (13%).
* 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 plyxp...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/print.R (line 209, column 3)
* 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 13
functions greater than 50 lines.
The longest 5 functions are:
summarize_se_impl() (R/dplyr-summarise.R): 169 lines
...
expand_across() (R/dplyr-across.R): 83 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
vectors.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; 111 lines (2%) are > 80 characters long.
First few lines:
R/connect_masks.R#L25 abort("could not reconstruct ...
...
vignettes/plyxp.Rmd#L358 the evaluation mask per dplyr verb. Try ...
i NOTE: Consider multiples of 4 spaces for line indents; 1683 lines (32%) are
not.
First few lines:
R/as.data.frame.R#L11 x <- se(x) ...
...
vignettes/plyxp.Rmd#L389 development team first through one of ...
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 Unable to connect to the Bioc-devel mailing list: HTTP 502 Bad Gateway.
* 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
0 ERRORS | 0 WARNINGS | 6 NOTES
i See the plyxp.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.