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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowClust.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowClust_3.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowClust.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowClust’ version ‘3.43.0’
* 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 ‘flowClust’ can be installed ... WARNING
Found the following significant warnings:
  coulomb.c:994:17: warning: variable 'G_lam_G' is uninitialized when used here [-Wuninitialized]
  coulomb.c:996:17: warning: variable 'Gp_lam_G' is uninitialized when used here [-Wuninitialized]
  exp.c:216:83: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  gamma.c:1614:54: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
  hyperg_1F1.c:1003:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1034:45: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1057:24: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1086:40: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1113:22: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1169:22: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1813:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1813:68: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1817:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_1F1.c:1817:66: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:285:38: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:527:13: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
  hyperg_U.c:861:45: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:871:11: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:881:11: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:913:38: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:947:39: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:998:35: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:1042:48: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:1108:49: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:1439:57: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  hyperg_U.c:1512:52: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  legendre_poly.c:544:67: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  legendre_poly.c:582:93: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  poch.c:164:46: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  poch.c:179:47: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./absdev_source.c:41:28: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  ./wabsdev_source.c:43:35: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  ldfrexp.c:63:13: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
  ldfrexp.c:88:12: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowClust.Rcheck/00install.out’ for details.
* 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 ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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:
    BUG FIXES
* 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
.flowClustK: no visible global function definition for ‘var’
.flowClustK: no visible global function definition for ‘qf’
.flowClustK: no visible global function definition for ‘qchisq’
.flowClustK: no visible global function definition for ‘quantile’
.flowClustK: no visible global function definition for ‘kmeans’
.hist.flowClust: no visible global function definition for ‘hist’
dmvt: no visible global function definition for ‘mahalanobis’
hist.flowClust: no visible global function definition for ‘hist’
hist.flowClust: no visible global function definition for ‘curve’
hist.flowClust: no visible global function definition for ‘stripchart’
hist.flowClustList: no visible global function definition for ‘hist’
plot,flowClust-missing: no visible global function definition for
  ‘gray’
plot,flowClust-missing: no visible global function definition for
  ‘hist’
plot,flowClust-missing: no visible global function definition for
  ‘title’
plot,flowClust-missing: no visible global function definition for
  ‘points’
plot,flowClust-missing: no visible global function definition for ‘qf’
plot,flowClust-missing: no visible global function definition for
  ‘qchisq’
plot,flowClustList-missing: no visible global function definition for
  ‘gray’
plot,flowDens-missing: no visible global function definition for
  ‘contour’
plot,flowDens-missing: no visible global function definition for
  ‘heat.colors’
plot,flowDens-missing: no visible global function definition for
  ‘rainbow’
plot,flowDens-missing: no visible global function definition for
  ‘terrain.colors’
plot,flowDens-missing: no visible global function definition for
  ‘topo.colors’
plot,flowDens-missing: no visible global function definition for
  ‘cm.colors’
plot,flowDens-missing: no visible global function definition for ‘gray’
plot,flowDens-missing: no visible global function definition for
  ‘image’
plot,flowFrame-tmixFilterResult: no visible global function definition
  for ‘hist’
ruleOutliers<-,flowClust-list: no visible global function definition
  for ‘qf’
ruleOutliers<-,flowClust-list: no visible global function definition
  for ‘qchisq’
Undefined global functions or variables:
  cm.colors contour curve gray heat.colors hist image kmeans
  mahalanobis points qchisq qf quantile rainbow stripchart
  terrain.colors title topo.colors var
Consider adding
  importFrom("grDevices", "cm.colors", "gray", "heat.colors", "rainbow",
             "terrain.colors", "topo.colors")
  importFrom("graphics", "contour", "curve", "hist", "image", "points",
             "stripchart", "title")
  importFrom("stats", "kmeans", "mahalanobis", "qchisq", "qf",
             "quantile", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'flowClust.Rd':
  ‘SimulateMixture’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 shell scripts ... 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 ... NOTE
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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowClust/libs/flowClust.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_printf’, possibly from ‘printf’ (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
* 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowClust.Rcheck/00check.log’
for details.