##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sincell.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sincell_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sincell.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sincell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sincell’ version ‘1.38.0’
* 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 ‘sincell’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN sincell 0.99.0:
      INITIAL RELEASE
* 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
sc_AssociationOfCellsHierarchyWithAGeneSet: no visible global function
  definition for ‘cor’
sc_ComparissonOfGraphs: no visible global function definition for ‘cor’
sc_ComparissonOfGraphs: no visible global function definition for
  ‘hclust’
sc_DimensionalityReductionObj: no visible global function definition
  for ‘prcomp’
sc_DimensionalityReductionObj: no visible global function definition
  for ‘cmdscale’
sc_GraphBuilderObj: no visible global function definition for ‘combn’
sc_InSilicoCellsReplicatesObj: no visible binding for global variable
  ‘var’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function
  definition for ‘runif’
sc_InSilicoCellsReplicatesObj : expressedvar: no visible global
  function definition for ‘var’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible binding for
  global variable ‘rnorm’
sc_InSilicoCellsReplicatesObj: no visible global function definition
  for ‘quantile’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function
  definition for ‘rnbinom’
sc_InitializingSincellObject: no visible binding for global variable
  ‘var’
sc_StatisticalSupportByGeneSubsampling: no visible global function
  definition for ‘cor’
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates: no
  visible global function definition for ‘cor’
sc_clusterObj: no visible global function definition for ‘hclust’
sc_clusterObj: no visible global function definition for ‘cutree’
sc_distanceObj: no visible global function definition for ‘cor’
sc_marker2color: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  cmdscale colorRampPalette combn cor cutree hclust prcomp quantile
  rnbinom rnorm runif var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "cmdscale", "cor", "cutree", "hclust", "prcomp",
             "quantile", "rnbinom", "rnorm", "runif", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/sincell/libs/sincell.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                                user system
sc_StatisticalSupportByGeneSubsampling                        60.334  2.690
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates  6.995  0.914
                                                              elapsed
sc_StatisticalSupportByGeneSubsampling                         19.231
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates   2.478
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/sincell.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sincell
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘sincell’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sstalgorithm.cpp -o sstalgorithm.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o sincell.so RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-sincell/00new/sincell/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (sincell)