===============================
R CMD BUILD
===============================
* checking for file MotifPeeker/DESCRIPTION ... OK
* preparing MotifPeeker:
* 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 MotifPeeker_0.99.10.tar.gz
===============================
BiocCheckGitClone('MotifPeeker')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker
BiocVersion: 3.20
Package: MotifPeeker
PackageVersion: 0.99.10
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker
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')
===============================
R CMD CHECK
===============================
* using log directory /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker.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 MotifPeeker/DESCRIPTION ... OK
* checking extension type ... Package
* this is package MotifPeeker version 0.99.10
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Imports includes 25 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 MotifPeeker 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [36s/37s] 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [97s/115s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MotifPeeker 38.986 4.760 43.468
motif_similarity 4.587 0.746 5.121
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [106s/134s]
[107s/134s] 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/4s] OK
* DONE
Status: 1 NOTE
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker.Rcheck/00check.log
for details.
===============================
BiocCheck('MotifPeeker_0.99.10.tar.gz')
===============================
Installing MotifPeeker
Package installed successfully
MotifPeeker session metadata
sourceDir: /tmp/RtmphwKX5g/file3def4d45608f4f/MotifPeeker
BiocVersion: 3.20
Package: MotifPeeker
PackageVersion: 0.99.10
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/b3cd64674a73d6fc572f247cf58dec6078419a0f/MotifPeeker.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmphwKX5g/file3def4d45608f4f/MotifPeeker
installDir: /tmp/RtmphwKX5g/file3def4d76190ec1
isTarBall: TRUE
platform: unix
Running BiocCheck on MotifPeeker
* 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 (50%).
* 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 MotifPeeker...
* Checking coding practice...
* 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 7
functions greater than 50 lines.
The longest 5 functions are:
MotifPeeker() (R/MotifPeeker.R): 140 lines
...
plot_motif_comparison() (R/plot_motif_comparison.R): 53 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; 24 lines (1%) are > 80 characters long.
First few lines:
R/calc_frip.R#L7 #' \deqn{\text{FRiP} = \frac{(\text{numb ...
...
vignettes/troubleshooting.Rmd#L42 Additionally, follow the [runtime gu ...
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 2 NOTES
i See the MotifPeeker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.