===============================
R CMD BUILD
===============================
* checking for file ‘gDRstyle/DESCRIPTION’ ... OK
* preparing ‘gDRstyle’:
* 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 ‘gDRstyle_0.99.1.tar.gz’
===============================
BiocCheckGitClone('gDRstyle')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: gDRstyle
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2976/44b57ebbd6a1b661e7ecc7c411b37600ac1e4ceb/gDRstyle
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
gDRstyle.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/2976/44b57ebbd6a1b661e7ecc7c411b37600ac1e4ceb/gDRstyle.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRstyle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRstyle’ version ‘0.99.1’
* 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 ‘gDRstyle’ can be installed ... WARNING
Found the following significant warnings:
Warning: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2976/44b57ebbd6a1b661e7ecc7c411b37600ac1e4ceb/gDRstyle.Rcheck/00install.out’ for details.
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘remotes:::version_satisfies_criteria’
See the note in ?`:::` about the use of this operator.
* 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 ‘gDRstyle-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkDependencies
> ### Title: Check for alignment of package dependencies across Rplatform and
> ### package specifications.
> ### Aliases: checkDependencies
>
> ### ** Examples
>
> checkDependencies(
+ dep_path = "gDRstyle/testdata/dependencies.yaml",
+ desc_path = "gDRstyle/"
+ )
Error in checkDependencies(dep_path = "gDRstyle/testdata/dependencies.yaml", :
'gDRstyle/testdata/dependencies.yaml' file not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [21s/27s]
[21s/27s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
❯ checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
What license is it under?
Standardizable: FALSE
0 errors ✔ | 1 warning ✖ | 1 note ✖
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 25 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-check.R:7:3'): package check works correct ───────────────────
Expected `checkPackage("fakePkg", dir, fail_on = "note")` to run without any errors.
i Actually got a <rcmdcheck_warning>:
Error:
! R CMD check found WARNINGs
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 25 ]
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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2976/44b57ebbd6a1b661e7ecc7c411b37600ac1e4ceb/gDRstyle.Rcheck/00check.log’
for details.
===============================
BiocCheck('gDRstyle_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: gDRstyle
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmpthum2l/file3dddb22d444fa/gDRstyle
─ installDir: /tmp/Rtmpthum2l/file3dddb26fc7903c
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2976/44b57ebbd6a1b661e7ecc7c411b37600ac1e4ceb/gDRstyle.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...
* 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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* 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 gDRstyle...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 1 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 289 lines
(27%) 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 | 4 NOTES
See the gDRstyle.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.