===============================
R CMD BUILD
===============================
* checking for file ‘faers/DESCRIPTION’ ... OK
* preparing ‘faers’:
* 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 ‘faers_0.99.0.tar.gz’
===============================
BiocCheckGitClone('faers')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: faers
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3227/faers_20231120161528/faers
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
faers.Rproj
* 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...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3227/faers_20231120161528/faers.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 ‘faers/DESCRIPTION’ ... OK
* this is package ‘faers’ 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 whether package ‘faers’ 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 ... [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 ... [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 ... [7s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/7s]
[11s/7s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
── Error ('test_methods.R:535:5'): `faers_modify()` for standardizated data works well ──
<no_dir/rlang_error/error/condition>
Error in `locate_dir(path, "^MedAscii$")`: Cannot locate ^MedAscii$ directory in
Backtrace:
▆
1. ├─faers::faers_standardize(...) at test_methods.R:535:5
2. └─faers::faers_standardize(...)
3. └─faers (local) .local(object, ...)
4. └─faers::meddra(meddra_path, add_smq = add_smq)
5. └─faers:::meddra_load_hierarchy(path, primary_soc = TRUE)
6. └─faers:::meddra_load(path, use = c("llt", "mdhier"))
7. ├─faers:::locate_files(locate_dir(path, "^MedAscii$"), "\\.asc$")
8. │ └─base::list.files(path, full.names = TRUE)
9. └─faers:::locate_dir(path, "^MedAscii$")
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
[ FAIL 17 | WARN 0 | SKIP 1 | PASS 274 ]
Error: Test failures
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 ... [4s/4s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3227/faers_20231120161528/faers.Rcheck/00check.log’
for details.
===============================
BiocCheck('faers_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: faers
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpEbPipX/file348fef13d4bd98/faers
─ installDir: /tmp/RtmpEbPipX/file348fef6abb0ddf
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3227/faers_20231120161528/faers.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 3.5.0 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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* 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 recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) 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 faers...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 10 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 20% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* 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...
* NOTE: Consider shorter lines; 166 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 54 lines
(1%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 12 NOTES
See the faers.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.