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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVP.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SVP_1.1.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SVP/DESCRIPTION' ... OK
* this is package 'SVP' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 whether package 'SVP' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... INFO
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.6Mb
    libs   1.9Mb
* 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 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 ... OK
* 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:
  LISAResult.Rd: SingleCellExperiment-class
  LISAsce-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  SVPExperiment.Rd: SingleCellExperiment, SingleCellExperiment-class
  cal_lisa_f1-method.Rd: SingleCellExperiment-class
  cluster.assign-method.Rd: SingleCellExperiment-class
  data_hpda_spe_cell_dec.Rd: SpatialExperiment-class
  data_sceSubPbmc.Rd: SingleCellExperiment-class
  extract_weight_adj-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  fscoreDfs.Rd: SingleCellExperiment-class, DataFrame-class, List-class
  gsvaExps.Rd: SingleCellExperiment-class, colData, List-class,
    assay<-, Annotated-class, metadata, Vector-class, mcols
  mob_sce.Rd: SingleCellExperiment-class
  pred.cell.signature-method.Rd: SingleCellExperiment-class
  runCORR-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  runDetectSVG-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class, SimpleList-class, DataFrame-class
  runENCODE-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  runGLOBALBV-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  runKldSVG-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class, SimpleList-class, DataFrame-class
  runLISA-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class, SimpleList-class
  runLOCALBV-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class, SimpleList-class
  runMCA-method.Rd: SingleCellExperiment-class
  runSGSA-method.Rd: SingleCellExperiment-class
  runWKDE-method.Rd: SingleCellExperiment-class,
    SpatialExperiment-class
  svDfs.Rd: SingleCellExperiment-class, DataFrame-class, List-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 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 ... INFO
GNU make is a SystemRequirements.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/SVP/libs/x64/SVP.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
runKldSVG-method 21.54   0.44    2.31
runSGSA-method   19.30   0.59   20.17
runWKDE-method    5.26   0.45    2.30
as_tbl_df         4.53   0.19    5.08
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck/00check.log'
for details.