===============================
R CMD BUILD
===============================
* checking for file DspikeIn/DESCRIPTION ... OK
* preparing DspikeIn:
* 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 DspikeIn_0.99.8.tar.gz
===============================
BiocCheckGitClone('DspikeIn')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/94b01ce7415403bfbefe48aac5a718a0ae9fcb25/DspikeIn
BiocVersion: 3.22
Package: DspikeIn
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/94b01ce7415403bfbefe48aac5a718a0ae9fcb25/DspikeIn.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/94b01ce7415403bfbefe48aac5a718a0ae9fcb25/DspikeIn
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* 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 v1.45.7 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3778/94b01ce7415403bfbefe48aac5a718a0ae9fcb25/DspikeIn.Rcheck
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file DspikeIn/DESCRIPTION ... OK
* checking extension type ... Package
* this is package DspikeIn version 0.99.8
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 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 DspikeIn can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking whether startup messages can be suppressed ... [13s/13s] 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 ... [46s/46s] 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 ... [11s/11s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('DspikeIn_0.99.8.tar.gz')
===============================
Installing DspikeIn
Package installed successfully
DspikeIn session metadata
sourceDir: /tmp/RtmpCr7WM9/file20cfcfe1871e5/DspikeIn
BiocVersion: 3.22
Package: DspikeIn
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/94b01ce7415403bfbefe48aac5a718a0ae9fcb25/DspikeIn.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /tmp/RtmpCr7WM9/file20cfcfe1871e5/DspikeIn
installDir: /tmp/RtmpCr7WM9/file20cfcf4b62e48c
isTarBall: TRUE
platform: unix
Running BiocCheck on DspikeIn
* 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...
i NOTE: Update R version dependency from 4.1.0 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: Classification
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 (30%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
Getting-started-with-DspikeIn.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DspikeIn...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/perform_and_visualize_DA.R (line 212, column 32)
R/perform_and_visualize_DA.R (line 228, column 29)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/RandomForest_selected.R (line 174, column 5)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/plotbar_abundance.R (line 92, column 12)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/adjust_abundance_one_third.R (line 35, column 33)
...
R/weight_Network.R (line 58, column 40)
* 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 36
functions greater than 50 lines.
The longest 5 functions are:
perform_and_visualize_DA() (R/perform_and_visualize_DA.R): 427 lines
...
alluvial_plot() (R/alluvial_plot.R): 170 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
detect_common_asvs_taxa.Rd
...
plotbar_abundance.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
Found in files:
detect_common_asvs_taxa.Rd
...
plotbar_abundance.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
detect_common_asvs_taxa.Rd
...
plotbar_abundance.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; 935 lines (10%) are > 80 characters long.
First few lines:
R/aaa-ExpData_class.R#L2 #' @description This is a virtual superc ...
...
vignettes/Getting-started-with-DspikeIn.Rmd#L1459 Quantitative PCR (qPCR) was
used to comp ...
i NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
First few lines:
vignettes/Getting-started-with-DspikeIn.Rmd#L320 Tip labels= OTU/ASV names
...
...
vignettes/Getting-started-with-DspikeIn.Rmd#L340 # Branch length numbers=
Actual evolutio ...
i NOTE: Consider multiples of 4 spaces for line indents; 2550 lines (26%) are
not.
First few lines:
R/accessors.R#L11 if (inherits(obj, "phyloseq")) { ...
...
vignettes/Getting-started-with-DspikeIn.Rmd#L1448 } ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.7 results
1 ERRORS | 0 WARNINGS | i 16 NOTES
i See the DspikeIn.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.