===============================
R CMD BUILD
===============================
* checking for file ‘chevreul/DESCRIPTION’ ... OK
* preparing ‘chevreul’:
* 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 ‘chevreul_0.99.11.tar.gz’
===============================
BiocCheckGitClone('chevreul')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/05d4fbb1aeda160e9030459247771a6ffbeaba3f/chevreul
─ BiocVersion: 3.20
─ Package: chevreul
─ PackageVersion: 0.99.11
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/05d4fbb1aeda160e9030459247771a6ffbeaba3f/chevreul.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/05d4fbb1aeda160e9030459247771a6ffbeaba3f/chevreul
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3332/05d4fbb1aeda160e9030459247771a6ffbeaba3f/chevreul.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chevreul/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chevreul’ version ‘0.99.11’
* 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 ‘chevreul’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [26s/26s] OK
* checking whether the package can be loaded with stated dependencies ... [26s/26s] OK
* checking whether the package can be unloaded cleanly ... [26s/26s] OK
* checking whether the namespace can be loaded with stated dependencies ... [26s/26s] OK
* checking whether the namespace can be unloaded cleanly ... [27s/27s] OK
* checking loading without being on the library search path ... [27s/27s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called 'batchelor'
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called 'scran'
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [87s/88s] NOTE
Found the following calls to data() loading into the global environment:
File ‘chevreul/R/chevreul_app.R’:
data("grch38_tx2gene")
File ‘chevreul/R/plotting.R’:
data(cc.genes.cyclone)
data("grch38")
data("grch38_tx2gene")
See section ‘Good practice’ in ‘?data’.
* 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 ... WARNING
Functions or methods with usage in Rd file 'pipe.Rd' but not in code:
'%>%'
* 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 ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [203s/222s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
regress_cell_cycle 18.338 0.495 19.143
find_all_markers 16.907 0.991 18.234
annotate_cell_cycle 13.267 1.052 14.756
add_percent_mito 7.738 1.251 10.057
object_reduce_dimensions 7.428 0.156 7.899
rename_object 0.863 0.089 7.622
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('chevreul_0.99.11.tar.gz')
===============================
* Installing package...
─ sourceDir: /tmp/RtmpZirZ7b/file85955af78364/chevreul
─ BiocVersion: 3.20
─ Package: chevreul
─ PackageVersion: 0.99.11
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/05d4fbb1aeda160e9030459247771a6ffbeaba3f/chevreul.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /tmp/RtmpZirZ7b/file85955af78364/chevreul
─ installDir: /tmp/RtmpZirZ7b/file85952fd348e4
─ isTarBall: TRUE
─ platform: unix
* 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...
* WARNING: Package files exceed the 5MB size limit.
* 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:
Transcriptomics, Normalization, Preprocessing, ImmunoOncology,
QualityControl, DimensionReduction, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (24%).
* Checking for pinned package versions in DESCRIPTION...
* 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 chevreul...
* 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...
* 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...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 14% of man pages use at least one of these tags.
* 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; 342 lines (5%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 53 lines (1%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 67 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...
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 | 1 WARNINGS | 11 NOTES
See the chevreul.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir chevreul_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘chevreul’ ...
** using staged installation
** R
** data
** 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 (chevreul)