===============================
R CMD BUILD
===============================
* checking for file ‘DunedinPACE/DESCRIPTION’ ... OK
* preparing ‘DunedinPACE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DunedinPACE.Rmd’ using rmarkdown
Quitting from lines 36-41 (DunedinPACE.Rmd)
Error: processing vignette 'DunedinPACE.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'assay': object 'example_betas' not found
--- failed re-building ‘DunedinPACE.Rmd’
SUMMARY: processing the following file failed:
‘DunedinPACE.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘DunedinPACE/DESCRIPTION’ ... OK
* preparing ‘DunedinPACE’:
* 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 ‘DunedinPACE_0.99.0.tar.gz’
===============================
BiocCheckGitClone('DunedinPACE')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DunedinPACE
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2789/DunedinPACE_20230120132115/DunedinPACE
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
DunedinPACE.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2789/DunedinPACE_20230120132115/DunedinPACE.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DunedinPACE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DunedinPACE’ 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 ‘DunedinPACE’ 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/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SummarizedExperiment’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] OK
* checking Rd files ... [1s/1s] NOTE
prepare_Rd: PACEProjector.Rd:26-28: Dropping empty section \source
prepare_Rd: getRequiredProbes.Rd:24-26: Dropping empty section \source
prepare_Rd: mPACE_Models.Rd:13-15: Dropping empty section \details
prepare_Rd: mPACE_Models.Rd:16-18: Dropping empty section \source
prepare_Rd: mPACE_Models.Rd:19-21: Dropping empty section \references
prepare_Rd: mPACE_Models.Rd:22-23: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘PoAmProjector’ ‘example_betas’
Undocumented data sets:
‘example_betas’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [12s/16s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
example_betas.rda 917Kb 744Kb xz
* checking R/sysdata.rda ... NOTE
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
sysdata.rda 342Kb 217Kb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] 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 ... [9s/11s] OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2789/DunedinPACE_20230120132115/DunedinPACE.Rcheck/00check.log’
for details.
===============================
BiocCheck('DunedinPACE_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DunedinPACE
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwbAX2M/file130b52a1d2a86/DunedinPACE
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwbAX2M/file130b532a5859e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2789/DunedinPACE_20230120132115/DunedinPACE.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* 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 4.3.0.
* 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:
Normalization
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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import SummarizedExperiment in NAMESPACE as well as
DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DunedinPACE...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages:
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 33% 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...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
Warning in .rmYAMLfm(lines) :
More than 2 YAML front matter delimiters, i.e., '---' found
* NOTE: Consider shorter lines; 56 lines (18%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 45 lines
(14%) 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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
3 ERRORS | 3 WARNINGS | 13 NOTES
See the DunedinPACE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DunedinPACE_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘DunedinPACE’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DunedinPACE)