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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mitoClone2_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/mitoClone2/libs/mitoClone2.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (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 36.188  0.804  37.056
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mitoClone2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
mkdir -p "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: '/*' within block comment [-Wcomment]
 /**************************************************************************************
 ^
bam2R_10x.cpp:8:1: warning: '/*' within block comment [-Wcomment]
/**********************************************************************
^
bam2R_10x.cpp:21:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:3:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
            int bc_absent;
                ^
bam2R_10x.cpp:53:9: warning: variable 'missingBC' set but not used [-Wunused-but-set-variable]
    int missingBC = 0;
        ^
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
    hts_itr_t *iter = NULL;
               ^
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
    int c = 0;
        ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mitoClone2.so bam2R_10x.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mitoClone2)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(mitoClone2)
> 
> test_check("mitoClone2")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  5.856   0.187   6.050