===============================
R CMD BUILD
===============================
* checking for file ‘PlinkMatrix/DESCRIPTION’ ... OK
* preparing ‘PlinkMatrix’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘PlinkMatrix/docs’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘PlinkMatrix_0.99.0.tar.gz’
===============================
BiocCheckGitClone('PlinkMatrix')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/PlinkMatrix_20260324153056/PlinkMatrix
→ BiocVersion: 3.23
→ Package: PlinkMatrix
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/PlinkMatrix_20260324153056/PlinkMatrix.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/PlinkMatrix_20260324153056/PlinkMatrix
→ 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...
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 v1.47.20 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/4182/PlinkMatrix_20260324153056/PlinkMatrix.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 15:33:29 UTC
* using option ‘--no-vignettes’
* checking for file ‘PlinkMatrix/DESCRIPTION’ ... OK
* this is package ‘PlinkMatrix’ version ‘0.99.0’
* 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 ‘PlinkMatrix’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [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 ... [25s/25s] NOTE
Found the following calls to data() loading into the global environment:
File ‘PlinkMatrix/R/cache_example.R’:
data("g445samples", package = "PlinkMatrix")
data("example_GRanges", package = "PlinkMatrix")
See section ‘Good practice’ in ‘?data’.
* 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [13s/14s]
[14s/14s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4182/PlinkMatrix_20260324153056/PlinkMatrix.Rcheck/00check.log’
for details.
===============================
BiocCheck('PlinkMatrix_0.99.0.tar.gz')
===============================
── Installing PlinkMatrix ──────────────────────────────────────────────────────
✔ Package installed successfully
── PlinkMatrix session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAw4KVr/file1744e42d81bdad/PlinkMatrix
→ BiocVersion: 3.23
→ Package: PlinkMatrix
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/PlinkMatrix_20260324153056/PlinkMatrix.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpAw4KVr/file1744e42d81bdad/PlinkMatrix
→ installDir: /tmp/RtmpAw4KVr/file1744e4f17b823
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PlinkMatrix ────────────────────────────────────────────
* 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 4.1.0 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 (75%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PlinkMatrix...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/plid2gr.R (line 13, column 22)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• decode_bed_genotypes.R (line 32, column 10)
• ...
• selectSome.R (line 12, column 64)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/cache_example.R (line 7, column 24)
• ...
• R/selectSome.R (line 1, column 12)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/decode_bed_genotypes.Rd
• ...
• man/show-PlinkSeed-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• PlinkMatrix.Rd
• PlinkSeed.Rd
• read_bed_subset.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 11 lines (2%) are > 80 characters long.
First few lines:
• R/cache_example.R#L8 url = "https://mghp.osn.xsede.org/bir1 ...
• ...
• vignettes/PlinkMatrix.Rmd#L30 - retrieve a zip archive from a cloud st ...
i NOTE: Consider multiples of 4 spaces for line indents; 95 lines (21%) are
not.
First few lines:
• R/cache_example.R#L8 url = "https://mghp.osn.xsede.org/bir1 ...
• ...
• vignettes/PlinkMatrix.Rmd#L74 rowData=example_GRanges, colData=g445 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.20 results ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | i 8 NOTES
i See the PlinkMatrix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.