===============================
R CMD BUILD
===============================
* checking for file ‘IdentifiHR/DESCRIPTION’ ... OK
* preparing ‘IdentifiHR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
* building ‘IdentifiHR_0.99.1.tar.gz’
===============================
BiocCheckGitClone('IdentifiHR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4186/IdentifiHR_20260324153123/IdentifiHR
→ BiocVersion: 3.23
→ Package: IdentifiHR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4186/IdentifiHR_20260324153123/IdentifiHR.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4186/IdentifiHR_20260324153123/IdentifiHR
→ 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 NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.47.20 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/4186/IdentifiHR_20260324153123/IdentifiHR.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-24 15:33:11 UTC
* using option ‘--no-vignettes’
* checking for file ‘IdentifiHR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdentifiHR’ 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 ‘IdentifiHR’ 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 ... [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 ... [7s/7s] 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 ... [23s/23s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
rawCounts.rda 939Kb 547Kb xz
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] 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
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4186/IdentifiHR_20260324153123/IdentifiHR.Rcheck/00check.log’
for details.
===============================
BiocCheck('IdentifiHR_0.99.1.tar.gz')
===============================
── Installing IdentifiHR ───────────────────────────────────────────────────────
✔ Package installed successfully
── IdentifiHR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvDuIsj/file173ed32dbef2c1/IdentifiHR
→ BiocVersion: 3.23
→ Package: IdentifiHR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4186/IdentifiHR_20260324153123/IdentifiHR.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpvDuIsj/file173ed32dbef2c1/IdentifiHR
→ installDir: /tmp/RtmpvDuIsj/file173ed34be871da
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IdentifiHR ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 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 (25%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• IdentifiHR.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of IdentifiHR...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/processCounts.R (line 130, column 12)
• ...
• R/processCounts.R (line 618, column 12)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
• processCounts() (R/processCounts.R): 601 lines
• interrogateMissingness() (R/interrogateMissingness.R): 131 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; 183 lines (16%) are > 80 characters long.
First few lines:
• R/internal_data.R#L7 # betaCoef - numeric vector of w ...
• ...
• vignettes/IdentifiHR.Rmd#L122 The Cancer Genome Atlas (TCGA) cohort of ...
i NOTE: Consider multiples of 4 spaces for line indents; 476 lines (41%) are
not.
First few lines:
• R/interrogateMissingness.R#L33 geneI ...
• ...
• vignettes/IdentifiHR.Rmd#L25 comment = "#>") ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.20 results ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the IdentifiHR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.