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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_0.99.6.tar.gz
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BiocCheckGitClone('parati')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/parati
BiocVersion: 3.23
Package: parati
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/parati.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/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 v1.47.20 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/parati.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 11:52:46 UTC
* using option --no-vignettes
* checking for file parati/DESCRIPTION ... OK
* checking extension type ... Package
* this is package parati version 0.99.6
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] 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 ... [0s/0s] ERROR
Running examples in parati-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: haplotype_infer
> ### Title: Infer parental transmitted and non-transmitted alleles
> ### Aliases: haplotype_infer
>
> ### ** Examples
>
> vcf_file <- system.file("extdata", "Toy_TrioGenotype.vcf.gz", package = "parati")
> vcf_dt <- read_vcf_by_chr(vcf_file, chr = 1)
Error in data.table::fread(file = vcf_file, skip = "#CHROM", sep = "\t", :
To read gz files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
Calls: read_vcf_by_chr -> <Anonymous> -> stopf -> raise_condition -> signal
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [1s/1s]
[1s/1s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Error ('test-haplotype_infer.R:5:3'): haplotype_infer returns expected columns
Error in `data.table::fread(file = vcf, skip = "#CHROM", sep = "\t", header = TRUE, data.table = TRUE, fill = TRUE)`: 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_read_vcf(vcf_file, chr = 1) at test-haplotype_infer.R:5:3
2. data.table::fread(...)
3. data.table:::stopf(...)
4. data.table:::raise_condition(...)
Error ('test-parati_run.R:6:3'): parati_run returns expected object structure
Error in `data.table::fread(file = vcf, skip = "#CHROM", sep = "\t", header = TRUE, data.table = TRUE, fill = TRUE)`: 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(vcf = vcf_file, fam = fam_file, chr = 1) at test-parati_run.R:6:3
2. parati:::.parati_read_vcf(vcf, chr = chr)
3. data.table::fread(...)
4. data.table:::stopf(...)
5. data.table:::raise_condition(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
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 ... [4s/4s] OK
* DONE
Status: 2 ERRORs
See
/home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/parati.Rcheck/00check.log
for details.
===============================
BiocCheck('parati_0.99.6.tar.gz')
===============================
Installing parati
Package installed successfully
parati session metadata
sourceDir: /tmp/RtmpTgLw3n/file1550c24f0655c2/parati
BiocVersion: 3.23
Package: parati
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4084/7756497153fa9652ba27c63430031395e636916c/parati.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpTgLw3n/file1550c24f0655c2/parati
installDir: /tmp/RtmpTgLw3n/file1550c29a3c7de
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...
* 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...
i Bioconductor dependencies found in Imports & Depends (50%).
* 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:
parati-workflow.Rmd
* 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 is 1
function greater than 50 lines.
The longest 5 functions are:
parati_run() (R/parati_run.R): 98 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; 17 lines (3%) are > 80 characters long.
First few lines:
R/haplotype_infer.R#L18 #' vcf_file <- system.file("extdata", "T ...
...
vignettes/parati-workflow.Rmd#L48 fam_file <- system.file("extdata", "Toy_
...
i NOTE: Consider multiples of 4 spaces for line indents; 195 lines (29%) are
not.
First few lines:
R/haplotype_infer.R#L27 vcf_dt, ...
...
vignettes/parati-workflow.Rmd#L81 hap_length = 500000 ...
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
1 ERRORS | 0 WARNINGS | i 6 NOTES
i See the parati.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.