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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_0.99.2.tar.gz
===============================
BiocCheckGitClone('PlinkMatrix')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/aaf4a64337a7105ec20c68c11e76c85aea457ff6/PlinkMatrix
BiocVersion: 3.23
Package: PlinkMatrix
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/aaf4a64337a7105ec20c68c11e76c85aea457ff6/PlinkMatrix.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/aaf4a64337a7105ec20c68c11e76c85aea457ff6/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/aaf4a64337a7105ec20c68c11e76c85aea457ff6/PlinkMatrix.Rcheck
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-31 12:29:21 UTC
* using option --no-vignettes
* checking for file PlinkMatrix/DESCRIPTION ... OK
* this is package PlinkMatrix version 0.99.2
* 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 ... [7s/7s] 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 ... [21s/21s] 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 ... [9s/9s] ERROR
Running examples in PlinkMatrix-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decode_bed_genotypes
> ### Title: Helper function to decode BED format
> ### Aliases: decode_bed_genotypes
> ### Keywords: internal
>
> ### ** Examples
>
> decode_bed_genotypes
Error: object 'decode_bed_genotypes' not found
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running test.R [12s/12s]
[12s/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 ERROR, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4182/aaf4a64337a7105ec20c68c11e76c85aea457ff6/PlinkMatrix.Rcheck/00check.log
for details.
===============================
BiocCheck('PlinkMatrix_0.99.2.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
Installing PlinkMatrix
Package installed successfully
PlinkMatrix session metadata
sourceDir: /tmp/RtmpPiTJCm/file31d6846390cdb/PlinkMatrix
BiocVersion: 3.23
Package: PlinkMatrix
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4182/aaf4a64337a7105ec20c68c11e76c85aea457ff6/PlinkMatrix.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpPiTJCm/file31d6846390cdb/PlinkMatrix
installDir: /tmp/RtmpPiTJCm/file31d6829b89267
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...
* 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 12, column 21)
* 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/dim-PlinkSeed-method.Rd
...
man/show-PlinkSeed-method.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; 13 lines (3%) are > 80 characters long.
First few lines:
R/cache_example.R#L9 url <- "https://mghp.osn.xsede.org/bir ...
...
vignettes/PlinkMatrix.Rmd#L64 pairs(pca$x[, 1:4], col = factor(g445sam ...
i NOTE: Consider multiples of 4 spaces for line indents; 102 lines (21%) are
not.
First few lines:
R/cache_example.R#L9 url <- "https://mghp.osn.xsede.org/bir ...
...
vignettes/PlinkMatrix.Rmd#L74 rowData = example_GRanges, colData = g ...
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 404 Not Found.
BiocCheck v1.47.20 results
1 ERRORS | 1 WARNINGS | i 5 NOTES
i See the PlinkMatrix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.