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R CMD BUILD
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* checking for file parati/DESCRIPTION ... OK
* preparing parati:
* 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 parati_0.99.0.tar.gz
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BiocCheckGitClone('parati')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati
BiocVersion: 3.23
Package: parati
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati
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 v1.47.18 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file parati/DESCRIPTION ... OK
* checking extension type ... Package
* this is package parati 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 serialization versions ... OK
* checking whether package parati 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [6s/6s] 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 files in vignettes ... OK
* checking examples ... [2s/2s] ERROR
Running examples in parati-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parati_run
> ### Title: Run parati inference workflow
> ### Aliases: parati_run
>
> ### ** Examples
>
> # Load required package
> library(parati)
> library(data.table)
Attaching package: data.table
The following object is masked from package:base:
%notin%
>
> # Paths to example data included in the package
> vcf_file <- system.file("extdata", "Toy_TrioGenotype.vcf.gz", package = "parati")
> fam_file <- system.file("extdata", "Toy_FamilyIndexTable.xlsx", package = "parati")
> out_dir <- file.path(tempdir(), "parati_example")
> dir.create(out_dir, showWarnings = FALSE)
>
> # Run parati workflow
> res <- parati_run(
+ geno_file = vcf_file,
+ fam_file = fam_file,
+ out_dir = out_dir,
+ chr = 1,
+ hap_length = 500000
+ )
Error in data.table::fread(geno_file) :
To read gz files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
Calls: parati_run -> <Anonymous> -> stopf -> raise_condition -> signal
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [3s/3s]
[3s/3s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
+ expect_true("vcf_nontrans" %in% names(res))
+ expect_true("sim_perc_summary" %in% names(res))
+ })
Error: minimal parati run works
Error in `data.table::fread(geno_file)`: To read gz files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
Backtrace:
1. parati::parati_run(...)
2. data.table::fread(geno_file)
3. data.table:::stopf(...)
4. data.table:::raise_condition(...)
Error:
! Test failed with 1 failure and 0 successes.
Backtrace:
1. testthat::test_that(...)
2. testthat:::test_code(code, parent.frame())
3. withr (local) `<fn>`()
4. reporter$end_test(context = reporter$.context, test = test)
5. cli::cli_abort(...)
6. rlang::abort(...)
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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs
See
/home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati.Rcheck/00check.log
for details.
===============================
BiocCheck('parati_0.99.0.tar.gz')
===============================
Installing parati
Package installed successfully
parati session metadata
sourceDir: /tmp/RtmpqLodCh/file1037f37d887dc7/parati
BiocVersion: 3.23
Package: parati
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/parati_20260210134241/parati.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpqLodCh/file1037f37d887dc7/parati
installDir: /tmp/RtmpqLodCh/file1037f31a5294f6
isTarBall: TRUE
platform: unix
Running BiocCheck on parati
* 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...
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 parati...
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
haplotype_infer() (R/haplotype_infer.R): 96 lines
parati_run() (R/parati_run.R): 88 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/vcf_to_plink.Rd
man/write_vcf_dt.Rd
man/write_vcf_obj.Rd
* 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; 20 lines (4%) are > 80 characters long.
First few lines:
R/haplotype_infer.R#L5 #' Given a VCF and family table, infer w ...
...
vignettes/parati-workflow.Rmd#L131 * Recommended pre-filtering: call rate,
...
i NOTE: Consider multiples of 4 spaces for line indents; 115 lines (24%) are
not.
First few lines:
R/haplotype_infer.R#L21 vcf_dt, ...
...
vignettes/parati-workflow.Rmd#L125 --out ./results/ ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/experiment
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/workflows
* 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 v1.47.18 results
1 ERRORS | 2 WARNINGS | i 5 NOTES
i See the parati.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.