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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scGPS_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scGPS.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scGPS’ version ‘1.21.0’
* 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 ‘scGPS’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
* 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
plot_reduced: no visible binding for global variable ‘..count..’
Undefined global functions or variables:
  ..count..
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CORE_bagging.Rd: SingleCellExperiment-class
  CORE_clustering.Rd: SingleCellExperiment-class
  CORE_subcluster.Rd: SingleCellExperiment-class
  bootstrap_parallel.Rd: SingleCellExperiment-class
  bootstrap_prediction.Rd: SingleCellExperiment-class
  clustering.Rd: SingleCellExperiment-class
  clustering_bagging.Rd: SingleCellExperiment-class
  new_scGPS_object.Rd: SingleCellExperiment-class
  new_summarized_scGPS_object.Rd: SingleCellExperiment-class
  predicting.Rd: SingleCellExperiment-class
  sub_clustering.Rd: SingleCellExperiment-class
  training.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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
annotate_clusters      137.587  0.402 138.313
find_markers            59.174  0.207  59.480
CORE_bagging            13.381  0.168  12.475
clustering_bagging      11.444  0.032  10.384
clustering               7.814  0.076   5.707
find_optimal_stability   6.766  0.044   4.614
plot_optimal_CORE        6.717  0.031   5.753
plot_reduced             6.516  0.048   6.581
tSNE                     5.902  0.008   5.924
plot_CORE                5.749  0.032   4.710
CORE_clustering          5.608  0.069   4.580
CORE_subcluster          5.553  0.024   4.459
find_stability           5.522  0.020   4.501
rand_index               5.455  0.044   4.365
summary_deviance         5.266  0.072   5.351
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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