===============================
R CMD BUILD
===============================
* checking for file ‘QRscore/DESCRIPTION’ ... OK
* preparing ‘QRscore’:
* 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 ‘QRscore_0.99.8.tar.gz’
===============================
BiocCheckGitClone('QRscore')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore
→ BiocVersion: 3.21
→ Package: QRscore
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore
→ 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/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore.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 ‘QRscore/DESCRIPTION’ ... OK
* this is package ‘QRscore’ version ‘0.99.8’
* 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 ‘QRscore’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE
.add_test_result: no visible binding for global variable ‘var’
.extract_and_format_results: no visible global function definition for
‘p.adjust’
.fit_and_validate_zinb: no visible global function definition for
‘pchisq’
.fit_and_validate_zinb: no visible global function definition for
‘logLik’
.pairwise_tests: no visible global function definition for ‘var’
.qrscore_flex_one_sample: no visible global function definition for
‘setNames’
.run_qrscore_two_sample: no visible global function definition for
‘wilcox.test’
QRscore_ZINB_nSamples: no visible global function definition for
‘pchisq’
computeweight_disp: no visible global function definition for ‘var’
computeweight_mean: no visible global function definition for ‘var’
rank_x: no visible global function definition for ‘runif’
Undefined global functions or variables:
logLik p.adjust pchisq runif setNames var wilcox.test
Consider adding
importFrom("stats", "logLik", "p.adjust", "pchisq", "runif",
"setNames", "var", "wilcox.test")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [230s/127s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
QRscoreGenetest 224.164 1.621 123.031
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/9s]
[10s/10s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore.Rcheck/00check.log’
for details.
===============================
BiocCheck('QRscore_0.99.8.tar.gz')
===============================
── Installing QRscore ──────────────────────────────────────────────────────────
✔ Package installed successfully
── QRscore session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIe8sEr/file19dd415cbe14b5/QRscore
→ BiocVersion: 3.21
→ Package: QRscore
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44/QRscore.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpIe8sEr/file19dd415cbe14b5/QRscore
→ installDir: /tmp/RtmpIe8sEr/file19dd412b0058c9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on QRscore ────────────────────────────────────────────────
* 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 4.4.0 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...
* 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 (14%).
* 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 QRscore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressMessages() in R/de_analysis.R (line 236, column 35)
* Checking function lengths...
* 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; 62 lines (3%) are not.
First few lines:
• R/de_analysis.R#L89 gene_vec, g ...
• ...
• R/utils.R#L616 less than 100. ...
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 4 NOTES
i See the QRscore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.