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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mitoClone2_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mitoClone2.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 ‘mitoClone2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mitoClone2’ version ‘1.13.0’
* 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 ‘mitoClone2’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 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
mitoPlot: no visible binding for global variable ‘gene’
Undefined global functions or variables:
  gene
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'mitoPlot.Rd':
mitoPlot
  Code: function(variants, patient = NULL, genome = "hg38",
                 customGenome = NULL, showLegend = TRUE, showLabel =
                 TRUE)
  Docs: function(variants, patient = NULL, genome = "hg38", showLegend
                 = TRUE, showLabel = TRUE)
  Argument names in code not in docs:
    customGenome
  Mismatches in argument names:
    Position: 4 Code: customGenome Docs: showLegend
    Position: 5 Code: showLegend Docs: showLabel

Codoc mismatches from Rd file 'mutationCallsFromCohort.Rd':
mutationCallsFromCohort
  Code: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL =
                 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10,
                 MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1,
                 USE.REFERENCE = TRUE, genome = "hg38", customGenome =
                 NULL)
  Docs: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL =
                 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10,
                 MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1,
                 USE.REFERENCE = TRUE, genome = "hg38")
  Argument names in code not in docs:
    customGenome

Codoc mismatches from Rd file 'mutationCallsFromExclusionlist.Rd':
mutationCallsFromExclusionlist
  Code: function(BaseCounts, lim.cov = 20, min.af = 0.2,
                 min.num.samples = 0.01 * length(BaseCounts),
                 min.af.universal = min.af, universal.var.cells = 0.95
                 * length(BaseCounts), exclusionlists.use =
                 exclusionlists, max.var.na = 0.5, max.cell.na = 0.95,
                 genome = "hg38", customDNA = NULL, ncores = 1, ...)
  Docs: function(BaseCounts, lim.cov = 20, min.af = 0.2,
                 min.num.samples = 0.01 * length(BaseCounts),
                 min.af.universal = min.af, universal.var.cells = 0.95
                 * length(BaseCounts), exclusionlists.use =
                 exclusionlists, max.var.na = 0.5, max.cell.na = 0.95,
                 genome = "hg38", ncores = 1, ...)
  Argument names in code not in docs:
    customDNA
  Mismatches in argument names:
    Position: 11 Code: customDNA Docs: ncores
    Position: 12 Code: ncores Docs: ...

* 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 R/sysdata.rda ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/mitoClone2/libs/mitoClone2.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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
varCluster 55.623  0.191   55.82
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/mitoClone2.Rcheck/00check.log’
for details.