===============================
R CMD BUILD
===============================
* checking for file ‘crisprShiny/DESCRIPTION’ ... OK
* preparing ‘crisprShiny’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘crisprShiny_0.99.4.tar.gz’
===============================
BiocCheckGitClone('crisprShiny')
===============================
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: crisprShiny
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3091/f9079bd894fccfe311ffed6d34c0fe7f198d75ba/crisprShiny
─ 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...
* NOTE: No CITATION file found. Bioconductor packages are not
required to have a CITATION file but it is useful both for users
and for tracking Bioconductor project-wide metrics. If you later
post a preprint or publish a paper about your Bioconductor
package, please add the details with a 'doi' argument in the
CITATION file's 'bibentry()'.
─ 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/3091/f9079bd894fccfe311ffed6d34c0fe7f198d75ba/crisprShiny.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprShiny/DESCRIPTION’ ... OK
* this is package ‘crisprShiny’ version ‘0.99.4’
* 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 ‘crisprShiny’ 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 ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [16s/16s] 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 ... [49s/49s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [14s/14s] NOTE
Note: found 6 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[16s/17s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ ├─crisprDesign::addNtcs(guideSetExample_basic, ntcs = ntcs) at tests/testthat/setup.R:16:1
15. │ └─crisprDesign::addNtcs(guideSetExample_basic, ntcs = ntcs)
16. │ └─crisprDesign (local) .local(object, ...)
17. │ └─crisprDesign:::.createNtcGuideSet(object, ntcs, newSeqinfo)
18. │ ├─crisprDesign::GuideSet(...)
19. │ │ └─crisprDesign:::.isBSGenome(bsgenome)
20. │ │ └─methods::is(bsgenome, "BSgenome")
21. │ ├─crisprDesign::bsgenome(object)
22. │ └─crisprDesign::bsgenome(object)
23. │ └─crisprDesign (local) .local(object, ...)
24. │ └─BSgenome::getBSgenome(out)
25. │ └─BSgenome:::.getBSgenomeObjectFromInstalledPkgname(genome, load.only = load.only)
26. │ └─BSgenome:::.stopOnAvailablePkg(genome)
27. │ └─base::stop(...)
28. └─base::.handleSimpleError(...)
29. └─testthat (local) h(simpleError(msg, call))
30. └─rlang::abort(...)
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3091/f9079bd894fccfe311ffed6d34c0fe7f198d75ba/crisprShiny.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprShiny_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: crisprShiny
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpmnA2xd/file2612b42538a798/crisprShiny
─ installDir: /tmp/RtmpmnA2xd/file2612b45a114999
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3091/f9079bd894fccfe311ffed6d34c0fe7f198d75ba/crisprShiny.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 4.3.0 to 4.4.0.
* 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 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...
* 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...
Bioconductor dependencies found in Imports & Depends (53%).
* Checking for pinned package versions in DESCRIPTION...
* 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 crisprShiny...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 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...
* NOTE: Consider shorter lines; 21 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 130 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the crisprShiny.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.