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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AneuFinder_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.34.0’
* 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 ‘AneuFinder’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 whether startup messages can be suppressed ... 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
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 line endings in C/C++/Fortran sources/headers ... 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
refineBreakpoints         72.569  0.683  83.527
simulateReads             63.887  3.128  84.976
heatmapAneuploidies       63.842  0.800  73.986
plotHeterogeneity         39.442  0.326  45.892
heatmapGenomewideClusters 35.043  0.368  38.777
karyotypeMeasures         31.121  0.270  35.874
heatmapGenomewide         30.194  0.253  36.477
correctGC                 27.480  2.765  36.349
annotateBreakpoints       19.241  0.347  25.312
getBreakpoints            15.913  0.447  17.892
consensusSegments         12.096  0.123  15.131
subsetByCNVprofile         7.428  0.019   8.339
getSCEcoordinates          7.357  0.039  10.090
findCNVs.strandseq         6.292  0.047   7.317
findCNVs                   5.733  0.293   7.025
variableWidthBins          5.853  0.032   6.528
loadFromFiles              4.574  0.011   5.481
clusterByQuality           3.622  0.030   5.426
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.