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R CMD BUILD
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* checking for file ‘notame/DESCRIPTION’ ... OK
* preparing ‘notame’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘notame_0.99.1.tar.gz’
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BiocCheckGitClone('notame')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame
→ BiocVersion: 3.21
→ Package: notame
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘notame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notame’ version ‘0.99.1’
* 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 ‘notame’ 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 ... NOTE
License stub is invalid DCF.
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking whether startup messages can be suppressed ... [8s/8s] 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 ... [32s/32s] OK
* checking Rd files ... [1s/1s] 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [301s/258s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
perform_correlation_tests 16.763 1.844 9.878
pls_da 15.473 0.221 15.695
muvr_analysis 13.181 0.313 13.497
visualizations 9.255 2.400 8.959
perform_non_parametric 5.587 2.460 5.129
perform_auc 6.236 1.389 3.929
pls 7.000 0.175 7.176
pca_bhattacharyya_dist 6.423 0.512 6.936
plot_effect_heatmap 4.474 1.502 3.664
impute_rf 5.166 0.161 5.330
plot_injection_lm 3.925 1.382 3.027
save_group_lineplots 5.117 0.140 5.257
save_batch_plots 4.679 0.332 5.011
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [119s/97s]
[119s/97s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
INFO [2025-03-30 15:37:34]
Drift correction results inspected, report:
Drift_corrected: 100%
INFO [2025-03-30 15:37:34]
Checking feature information
INFO [2025-03-30 15:37:34] Checking that feature IDs are unique and not storedas numbers
INFO [2025-03-30 15:37:34] Checking that feature data includes a 'Split' column
INFO [2025-03-30 15:37:34] Checking that feature data includes a 'Flag' column
INFO [2025-03-30 15:37:34] Checking that feature abundances only contain numeric values
INFO [2025-03-30 15:37:34] Setting row and column names of exprs based on feature and pheno data
[ FAIL 1 | WARN 185 | SKIP 0 | PASS 219 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plotting.R:111:3'): Batch plots work with and without multiple assays ──
Error: Bioconductor package RUVSeq needed for this function to work. Please install it.
Backtrace:
▆
1. └─notame::ruvs_qc(example_set, replicates = replicates, name = "bcorrected") at test_plotting.R:111:3
[ FAIL 1 | WARN 185 | SKIP 0 | PASS 219 ]
Error: Test failures
Execution halted
* 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 ... [8s/8s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame.Rcheck/00check.log’
for details.
===============================
BiocCheck('notame_0.99.1.tar.gz')
===============================
── Installing notame ───────────────────────────────────────────────────────────
✔ Package installed successfully
── notame session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiZrufY/file153332642a7050/notame
→ BiocVersion: 3.21
→ Package: notame
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3751/ed74b6b3e17905a29e4c61ba0ac2f35677636cd1/notame.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpiZrufY/file153332642a7050/notame
→ installDir: /tmp/RtmpiZrufY/file1533324556520c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on notame ─────────────────────────────────────────────────
* 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 4.5.0 to 4.6.0.
* 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: Sequencing,
Coverage
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 (20%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of notame...
* Checking coding practice...
* 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 34
functions greater than 50 lines.
The longest 5 functions are:
• muvr_analysis() (R/multivariate.R): 120 lines
• ...
• perform_correlation_tests() (R/stats.R): 84 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 multiples of 4 spaces for line indents; 3578 lines (33%) are
not.
First few lines:
• R/batch_correction.R#L28 if (!requireNamespace("RUVSeq", quietl ...
• ...
• vignettes/project_example.Rmd#L234 rf_importance[, c("Feature_ID", "MeanD ...
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 v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the notame.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.