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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ncdfFlow_2.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.40.0’
* 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 ‘ncdfFlow’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.6Mb
    libs   3.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Invalid license file pointers: LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘BH’ ‘RcppArmadillo’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘flowCore:::check_channel_alias’ ‘flowCore:::guid’
  ‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’
  ‘flowCore:::update_channel_by_alias’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs =
  matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]),
  keyword(x[[guid]])), env = e1): partial argument match of 'env' to
  'envir'
rbind2,ncdfFlowList-ANY : <anonymous> : <anonymous>: warning in
  assign(curSample, NA, env = indiceEnv): partial argument match of
  'env' to 'envir'
read.ncdfFlowSet: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ncdfFlow/libs/ncdfFlow.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (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. 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 elapsed
Indices 7.08  0.322   7.468
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.