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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:tricycle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings tricycle_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tricycle.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tricycle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tricycle’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘tricycle’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... NOTE
circle_scale_legend: no visible binding for global variable ‘x1’
circle_scale_legend: no visible binding for global variable ‘y1’
circle_scale_legend: no visible binding for global variable ‘x2’
circle_scale_legend: no visible binding for global variable ‘y2’
plot_ccposition_den: no visible binding for global variable ‘x’
Undefined global functions or variables:
  x x1 x2 y1 y2
* checking Rd files ... NOTE
checkRd: (-1) estimate_cycle_position.Rd:26: Lost braces; missing escapes or markup?
    26 | and stored with name \code{dimred} in {x}. Default: 'tricycleEmbedding'}
       |                                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_Schwabe_stage.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  estimate_cycle_position.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  neurosphere_example.Rd: SingleCellExperiment-class
  plot_emb_circle_scale.Rd: SingleCellExperiment-class
  project_cycle_space.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  run_pca_cc_genes.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
run_pca_cc_genes 5.116  0.518   5.634
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/tricycle.Rcheck/00check.log’
for details.