===============================
R CMD BUILD
===============================
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* preparing ‘RAIDS’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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 ‘RAIDS_0.99.7.tar.gz’
===============================
BiocCheckGitClone('RAIDS')
===============================
─ BiocCheckVersion: 1.37.9
─ BiocVersion: 3.18
─ Package: RAIDS
─ PackageVersion: 0.99.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2995/1c50b6535e5531d82934664fa5a2a41a4c2cc77f/RAIDS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2995/1c50b6535e5531d82934664fa5a2a41a4c2cc77f/RAIDS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘0.99.7’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RAIDS’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the package can be unloaded cleanly ... [16s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [15s/15s] 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 ... [53s/53s] OK
* checking Rd files ... [1s/1s] 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 ... [69s/69s] ERROR
Running examples in ‘RAIDS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pruning1KGbyChr
> ### Title: Extract the pruned SNVs in a population reference data set
> ### (ex:1KG) by chromosome and/or allelic frequency
> ### Aliases: pruning1KGbyChr
> ### Keywords: internal
>
> ### ** Examples
>
>
> ## Required library
> library(SNPRelate)
>
> ## Path to the demo pedigree file is located in this package
> dataDir <- system.file("extdata", package="RAIDS")
>
> ## The 1KG Population Reference GDS demo file (opened)
> gds1KG <- snpgdsOpen(file.path(dataDir, "1KG_Demo.gds"))
>
> ## The prefix of the RDS file to be created and containing the pruned SNVs
> outPrefix <- "Pruned_Demo_Reference"
>
> ## Run only if directory in writing mode
> if (file.access(getwd()) == 0 &&
+ !file.exists(file.path(getwd(), paste0(outPrefix, ".rds")))) {
+
+ ## Create a RDS file with the pruned SNVs
+ RAIDS:::pruning1KGbyChr(gdsReference=gds1KG, outPrefix=outPrefix)
+
+ prunedSNVs <- readRDS(file.path(getwd(), paste0(outPrefix, ".rds")))
+ prunedSNVs
+
+ ## Delete temporary file
+ unlink(getwd(), paste0(outPrefix, ".rds"), force=TRUE)
+ }
Error in unlink(getwd(), paste0(outPrefix, ".rds"), force = TRUE) :
invalid 'recursive' argument
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [30s/30s]
[30s/30s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/6s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2995/1c50b6535e5531d82934664fa5a2a41a4c2cc77f/RAIDS.Rcheck/00check.log’
for details.
===============================
BiocCheck('RAIDS_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.37.9
─ BiocVersion: 3.18
─ Package: RAIDS
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/Rtmp8iiS6w/file12565c15e891e6/RAIDS
─ installDir: /tmp/Rtmp8iiS6w/file12565c5fa38cdf
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2995/1c50b6535e5531d82934664fa5a2a41a4c2cc77f/RAIDS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
BiocViews, GenomeWideAssociation, QualityControl, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'Apache License (>= 2)' unknown; licenses cannot
restrict use
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 RAIDS...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 36 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 2% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 116 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 587 lines
(3%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 13 NOTES
See the RAIDS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.