teran2 Summary
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| Package: XAItest |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data XAItest |
| BuildTime: 4 minutes 58.68 seconds |
| CheckCommand: BiocCheckGitClone('XAItest') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/R-libs --install=check:/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.install-out.txt XAItest_0.99.3.tar.gz && BiocCheck('XAItest_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 40.10 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1085.31 KiB |
| BuildID:: XAItest_20240919055458 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: XAItest. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
teran2 BUILD SRC output
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===============================
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_0.99.3.tar.gz’
teran2 CHECK output
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===============================
BiocCheckGitClone('XAItest')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest
→ BiocVersion: 3.20
→ Package: XAItest
→ PackageVersion: 0.99.3
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.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 ‘XAItest/DESCRIPTION’ ... OK
* this is package ‘XAItest’ version ‘0.99.3’
* 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 ... 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] 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 ... NOTE
Namespaces in Imports field not imported from:
‘RUnit’ ‘S4Vectors’ ‘SummarizedExperiment’
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 ... [3s/3s] NOTE
.findGM: no visible global function definition for ‘t.test’
.findNoiseSD: no visible global function definition for ‘cor.test’
.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’
contXAI: 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 ‘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’
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 xlab ylab
Consider adding
importFrom("methods", "is", "new")
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 ... NOTE
Rd file 'getFeatImpThresholds.Rd':
\examples lines wider than 100 characters:
# Assuming `df` is a dataframe with columns `feature1_pval`, `feature2_pval`, `feature1_imp`, `feature2_imp`
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'modelsOverview.Rd'
‘verbose’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [79s/76s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XAI.test 32.075 0.991 31.503
modelsOverview 30.929 0.443 30.270
plotModel 8.874 0.115 8.171
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘BiocGenerics’
* checking tests ...
Running ‘runTests.R’ [4s/4s]
[4s/4s] 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 ... [2s/2s] OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.Rcheck/00check.log’
for details.
===============================
BiocCheck('XAItest_0.99.3.tar.gz')
===============================
── Installing XAItest ──────────────────────────────────────────────────────────
✔ Package installed successfully
── XAItest session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRp0aDb/file2dc94322437371/XAItest
→ BiocVersion: 3.20
→ Package: XAItest
→ PackageVersion: 0.99.3
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpRp0aDb/file2dc94322437371/XAItest
→ installDir: /tmp/RtmpRp0aDb/file2dc94364f17090
→ 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 4.4.0.
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (30%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/XAItest.Rmd (code line 25, column 70)
• vignettes/XAItest.Rmd (code line 137, column 56)
• vignettes/XAItest.Rmd (code line 196, column 52)
* 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 sapply(); use vapply()
Found in files:
• R/getFeatImpThresholds.R (line 59, column 16)
• R/modelsOverview.R (line 64, column 20)
• R/modelsOverview.R (line 103, column 20)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• allClasses.R (line 22, column 39)
• ...
• XAI.test.R (line 619, column 21)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/modelsOverview.R (line 53, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/XAI.test.R (line 366, column 22)
• ...
• R/XAI.test.R (line 645, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 1 times:
• T in R/XAI.test.R (line 342, column 81)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• XAI.test.R (line 137, column 28)
• XAI.test.R (line 407, column 24)
* 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): 109 lines
• ...
• modelsOverview() (R/modelsOverview.R): 75 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/modelsOverview.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; 148 lines (11%) are > 80 characters long.
First few lines:
• R/getFeatImpThresholds.R#L1 #' The getFeatImpThresholds function ide ...
• ...
• vignettes/XAItest.Rmd#L313 The *mapPvalImportance* function reveals ...
i NOTE: Consider multiples of 4 spaces for line indents; 30 lines (2%) are not.
First few lines:
• R/mapPvalImportance.R#L54 if(is.numeric(x)) signif(x, digits ...
• ...
• vignettes/XAItest.Rmd#L310 ) ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | • 10 NOTES
i See the XAItest.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
teran2 BUILD BIN output
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nebbiolo2 Summary
[top]
| Package: XAItest |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data XAItest |
| BuildTime: 5 minutes 48.21 seconds |
| CheckCommand: BiocCheckGitClone('XAItest') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3519/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.install-out.txt XAItest_0.99.3.tar.gz && BiocCheck('XAItest_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 2.72 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 949.94 KiB |
| BuildID:: XAItest_20240919055458 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: XAItest. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
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_0.99.3.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('XAItest')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest
→ BiocVersion: 3.20
→ Package: XAItest
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.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 ‘XAItest/DESCRIPTION’ ... OK
* this is package ‘XAItest’ version ‘0.99.3’
* 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 ... 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] 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 ... NOTE
Namespaces in Imports field not imported from:
‘RUnit’ ‘S4Vectors’ ‘SummarizedExperiment’
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’
.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’
contXAI: 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 ‘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’
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 xlab ylab
Consider adding
importFrom("methods", "is", "new")
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 ... NOTE
Rd file 'getFeatImpThresholds.Rd':
\examples lines wider than 100 characters:
# Assuming `df` is a dataframe with columns `feature1_pval`, `feature2_pval`, `feature1_imp`, `feature2_imp`
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'modelsOverview.Rd'
‘verbose’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [96s/92s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XAI.test 39.579 1.370 39.068
modelsOverview 36.268 0.111 34.705
plotModel 12.420 0.075 11.573
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘BiocGenerics’
* checking tests ...
Running ‘runTests.R’ [5s/5s]
[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: 2 WARNINGs, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.Rcheck/00check.log’
for details.
===============================
BiocCheck('XAItest_0.99.3.tar.gz')
===============================
── Installing XAItest ──────────────────────────────────────────────────────────
✔ Package installed successfully
── XAItest session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQC7WRN/file2301da1456ddc3/XAItest
→ BiocVersion: 3.20
→ Package: XAItest
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3519/d0fe83e715ca1ba6f4aee039eec37b18d528bf9c/XAItest.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpQC7WRN/file2301da1456ddc3/XAItest
→ installDir: /tmp/RtmpQC7WRN/file2301dada0557
→ 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 4.4.0.
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (30%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/XAItest.Rmd (code line 25, column 70)
• vignettes/XAItest.Rmd (code line 137, column 56)
• vignettes/XAItest.Rmd (code line 196, column 52)
* 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 sapply(); use vapply()
Found in files:
• R/getFeatImpThresholds.R (line 59, column 16)
• R/modelsOverview.R (line 64, column 20)
• R/modelsOverview.R (line 103, column 20)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• allClasses.R (line 22, column 39)
• ...
• XAI.test.R (line 619, column 21)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/modelsOverview.R (line 53, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/XAI.test.R (line 366, column 22)
• ...
• R/XAI.test.R (line 645, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 1 times:
• T in R/XAI.test.R (line 342, column 81)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• XAI.test.R (line 137, column 28)
• XAI.test.R (line 407, column 24)
* 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): 109 lines
• ...
• modelsOverview() (R/modelsOverview.R): 75 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/modelsOverview.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; 148 lines (11%) are > 80 characters long.
First few lines:
• R/getFeatImpThresholds.R#L1 #' The getFeatImpThresholds function ide ...
• ...
• vignettes/XAItest.Rmd#L313 The *mapPvalImportance* function reveals ...
i NOTE: Consider multiples of 4 spaces for line indents; 30 lines (2%) are not.
First few lines:
• R/mapPvalImportance.R#L54 if(is.numeric(x)) signif(x, digits ...
• ...
• vignettes/XAItest.Rmd#L310 ) ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | • 10 NOTES
i See the XAItest.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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