===============================
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_0.99.10.tar.gz’
===============================
BiocCheckGitClone('XAItest')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/XAItest
→ BiocVersion: 3.21
→ Package: XAItest
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/XAItest.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/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/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/XAItest.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘XAItest/DESCRIPTION’ ... OK
* this is package ‘XAItest’ version ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.lintr
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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] NOTE
Warning: no function found corresponding to methods exports from ‘XAItest’ for: ‘show’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... NOTE
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘RUnit’ ‘S4Vectors’ ‘SummarizedExperiment’ ‘ggplot2’
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 ... [4s/4s] NOTE
.findGM: no visible global function definition for ‘t.test’
.findNoiseSD: no visible global function definition for ‘cor.test’
.objXAI: no visible global function definition for ‘new’
.regRNorm: no visible global function definition for ‘qnorm’
XAI.test: no visible global function definition for ‘is’
XAI.test: no visible global function definition for ‘assay’
XAI.test: no visible global function definition for ‘colData’
XAI.test: no visible global function definition for ‘new’
featureImportanceRF: no visible global function definition for
‘as.formula’
featureImportanceShap: no visible global function definition for
‘as.formula’
featureImportanceShap: no visible global function definition for
‘predict’
genSimulatedFeatures: no visible global function definition for ‘rnorm’
genSimulatedFeaturesRegr: no visible global function definition for
‘rnorm’
mapPvalImportance: no visible global function definition for ‘is’
modelsOverview: no visible global function definition for ‘is’
modelsOverview : <anonymous>: no visible global function definition for
‘predict’
pValCor : <anonymous>: no visible global function definition for
‘cor.test’
pValCor: no visible global function definition for ‘p.adjust’
pValEBayes: no visible global function definition for ‘as.formula’
pValEBayes: no visible global function definition for ‘model.matrix’
pValLM: no visible global function definition for ‘is’
pValLM: no visible global function definition for ‘as.formula’
pValLM: no visible global function definition for ‘lm’
pValLM: no visible global function definition for ‘p.adjust’
pValTTest : <anonymous>: no visible global function definition for
‘t.test’
pValTTest: no visible global function definition for ‘p.adjust’
plotModel: no visible global function definition for ‘is’
plotModel: no visible global function definition for ‘predict’
plotModel: no visible global function definition for ‘ggplot’
plotModel: no visible global function definition for ‘aes’
plotModel: no visible binding for global variable ‘Predictions’
plotModel: no visible global function definition for ‘geom_point’
plotModel: no visible global function definition for ‘theme_bw’
plotModel: no visible global function definition for ‘xlab’
plotModel: no visible global function definition for ‘ylab’
plotModel: no visible global function definition for ‘ggtitle’
setMetricsTable,ObjXAI: no visible global function definition for
‘validObject’
Undefined global functions or variables:
Predictions aes as.formula assay colData cor.test geom_point ggplot
ggtitle is lm model.matrix new p.adjust predict qnorm rnorm t.test
theme_bw validObject xlab ylab
Consider adding
importFrom("methods", "is", "new", "validObject")
importFrom("stats", "as.formula", "cor.test", "lm", "model.matrix",
"p.adjust", "predict", "qnorm", "rnorm", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented S4 methods:
generic 'getMetricsTable' and siglist 'ObjXAI'
generic 'setMetricsTable' and siglist 'ObjXAI'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [87s/83s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
modelsOverview 35.152 0.349 33.799
XAI.test 34.274 1.127 33.565
plotModel 10.858 0.052 10.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/XAItest.Rcheck/00check.log’
for details.
===============================
BiocCheck('XAItest_0.99.10.tar.gz')
===============================
── Installing XAItest ──────────────────────────────────────────────────────────
✔ Package installed successfully
── XAItest session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9sNSvN/file1097f34f78889/XAItest
→ BiocVersion: 3.21
→ Package: XAItest
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/9f358b2be69f7a139d5a192b6bac025265aa85d7/XAItest.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmp9sNSvN/file1097f34f78889/XAItest
→ installDir: /tmp/Rtmp9sNSvN/file1097f6b9f36a5
→ 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 (33%).
* 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 XAItest...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• allClasses.R (line 99, column 35)
• ...
• XAI.test.R (line 685, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/XAI.test.R (line 420, column 22)
• ...
• 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 55, 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...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/modelsOverview.Rd
• man/show-ObjXAI-method.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; 3 lines (0%) are > 80 characters long.
First few lines:
• R/allClasses.R#L52 setGeneric("getMetricsTable", function(o ...
• R/allClasses.R#L76 #' setMetricsTable(obj, data.frame(Metri ...
• R/allClasses.R#L79 setGeneric("setMetricsTable", function(o ...
i NOTE: Consider multiples of 4 spaces for line indents; 40 lines (2%) are not.
First few lines:
• R/allClasses.R#L21 "ObjXAI", ...
• ...
• vignettes/XAItest.Rmd#L212 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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 8 NOTES
i See the XAItest.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.