===============================
R CMD BUILD
===============================
* checking for file BatChef/DESCRIPTION ... OK
* preparing BatChef:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building BatChef_0.99.6.tar.gz
===============================
BiocCheckGitClone('BatChef')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef
BiocVersion: 3.22
Package: BatChef
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef
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 NAMESPACE...
* 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 v1.45.20 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/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef.Rcheck
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file BatChef/DESCRIPTION ... OK
* checking extension type ... Package
* this is package BatChef version 0.99.6
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 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 BatChef can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ... [21s/20s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/19s] OK
* checking whether the package can be unloaded cleanly ... [20s/19s] OK
* checking whether the namespace can be loaded with stated dependencies ... [20s/19s] OK
* checking whether the namespace can be unloaded cleanly ... [21s/20s] OK
* checking loading without being on the library search path ... [23s/23s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: withr
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [65s/63s] 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [104s/102s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
adjusted_rand_index 12.588 0.563 12.758
seuratV3Run 9.693 0.280 9.973
seuratV5Run 5.065 0.129 5.194
scMerge2Run 4.993 0.175 5.169
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [60s/176s]
[60s/176s] 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 ... [4s/4s] OK
* DONE
Status: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('BatChef_0.99.6.tar.gz')
===============================
Installing BatChef
Package installed successfully
BatChef session metadata
sourceDir: /tmp/RtmprOBp1t/file117a0154bb9b4a/BatChef
BiocVersion: 3.22
Package: BatChef
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3968/02fe8d15c86ea2ed350b709428841b2ff7ad2a53/BatChef.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /tmp/RtmprOBp1t/file117a0154bb9b4a/BatChef
installDir: /tmp/RtmprOBp1t/file117a0174cc9496
isTarBall: TRUE
platform: unix
Running BiocCheck on BatChef
* 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 4.1.0 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: Clustering
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 (44%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
batch_correction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BatChef...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/warnings.R (line 5, column 18)
R/wasserstein_distance.R (line 36, column 12)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
BatChefParams.R (line 74, column 51)
...
wasserstein_distance.R (line 46, column 16)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/merge_params.R (line 13, column 13)
* 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:
simulate_data() (R/simulate_data.R): 102 lines
...
fun() (R/leiden_clustering.R): 51 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
BatChefParams.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; 96 lines (4%) are > 80 characters long.
First few lines:
R/adjusted_rand_index.R#L26 #' compute_pca = TR ...
...
vignettes/batch_correction.Rmd#L44 Also, it provides metrics to evaluate th
...
i NOTE: Consider multiples of 4 spaces for line indents; 690 lines (26%) are
not.
First few lines:
R/adjusted_rand_index.R#L32 adata <- leiden_clustering(input = inp ...
...
vignettes/batch_correction.Rmd#L151 ...
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 v1.45.20 results
0 ERRORS | 0 WARNINGS | i 11 NOTES
i See the BatChef.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.