===============================
R CMD BUILD
===============================
* checking for file XAItest/DESCRIPTION ... OK
* preparing XAItest:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
XAItest/inst/extdata/seClassif.rds
XAItest/inst/extdata/seRegress.rds
* building XAItest_0.99.21.tar.gz
===============================
BiocCheckGitClone('XAItest')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/db3a6f121ebc1416cedb11b8d411526d3476b342/XAItest
BiocVersion: 3.21
Package: XAItest
PackageVersion: 0.99.21
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/db3a6f121ebc1416cedb11b8d411526d3476b342/XAItest.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/db3a6f121ebc1416cedb11b8d411526d3476b342/XAItest
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 /home/pkgbuild/packagebuilder/workers/jobs/3519/db3a6f121ebc1416cedb11b8d411526d3476b342/XAItest.Rcheck
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file XAItest/DESCRIPTION ... OK
* this is package XAItest 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 XAItest 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] 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 files in vignettes ... OK
* checking examples ... [86s/82s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
modelsOverview 34.680 0.235 33.179
XAI.test 33.609 1.049 33.033
plotModel 10.574 0.129 9.841
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTests.R [6s/6s]
[6s/6s] 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('XAItest_0.99.21.tar.gz')
===============================
Installing XAItest
Package installed successfully
XAItest session metadata
sourceDir: /tmp/RtmpvMgyKv/file29310a42d2fe97/XAItest
BiocVersion: 3.21
Package: XAItest
PackageVersion: 0.99.21
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/db3a6f121ebc1416cedb11b8d411526d3476b342/XAItest.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpvMgyKv/file29310a42d2fe97/XAItest
installDir: /tmp/RtmpvMgyKv/file29310a399a5f2c
isTarBall: TRUE
platform: unix
Running BiocCheck on XAItest
* 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 3.5.0 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...
* 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 (22%).
* Checking for pinned package versions in DESCRIPTION...
ERROR: Dependencies in the DESCRIPTION file contain '=='
* 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 XAItest...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
allClasses.R (line 104, column 35)
...
XAI.test.R (line 685, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/plotModel.R (line 53, column 17)
...
R/XAI.test.R (line 712, column 22)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/modelsOverview.R (line 59, column 17)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/XAItest.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
The longest 5 functions are:
XAI.test() (R/XAI.test.R): 124 lines
...
.XAIregress() (R/XAI.test.R): 81 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; 7 lines (0%) are > 80 characters long.
First few lines:
R/allClasses.R#L54 setGeneric("getMetricsTable", function(o ...
...
vignettes/XAItest.Rmd#L322 mpi <- mapPvalImportance(regr_results, r ...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
R/plotModel.R#L99 ggplot2::aes(x = x, y = y, col ...
R/plotModel.R#L130 ggplot2::aes(x = x, y = y, colo ...
i NOTE: Consider multiples of 4 spaces for line indents; 38 lines (2%) are not.
First few lines:
R/allClasses.R#L21 "ObjXAI", ...
...
vignettes/XAItest.Rmd#L219 simData=TRUE) ...
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
1 ERRORS | 0 WARNINGS | i 9 NOTES
i See the XAItest.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.