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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PING.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PING_2.50.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PING.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PING/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PING’ version ‘2.50.0’
* 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 ‘PING’ can be installed ... WARNING
Found the following significant warnings:
  ping.c:145:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ping.c:3408:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PING.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package 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 ... NOTE
Warning: no function found corresponding to methods exports from 'PING' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BSgenome' 'BiocGenerics' 'GenomicRanges' 'IRanges' 'S4Vectors' 'fda'
  'methods' 'stats' 'stats4'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,ping-segReads: warning in symbols((map[, 1] + map[, 2])/2,
  rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6,
  nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim =
  c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to
  'rectangles'
plot,ping-segReads : <anonymous>: warning in symbols(x@estimates$mu +
  shift * se(x), rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol =
  2, byrow = TRUE), inches = FALSE, bg = 0, fg = grey(abs(shift) *
  se(x)/(3 * (se(x)))), add = TRUE, xlim = c(m, M), ylim = c(0, 1), lwd
  = 2): partial argument match of 'rec' to 'rectangles'
plot,ping-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
  = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
  FALSE, bg = "white", fg = grey(abs(0)), add = TRUE, xlim = c(m, M),
  ylim = c(0, 1)): partial argument match of 'rec' to 'rectangles'
CoverageTrack: no visible global function definition for 'resize'
CoverageTrack: no visible global function definition for 'seqnames'
CoverageTrack: no visible global function definition for 'start'
CoverageTrack: no visible global function definition for 'coverage'
CoverageTrack: no visible global function definition for 'width'
FilterPING: no visible global function definition for 'quantile'
NucleosomeTrack: no visible global function definition for 'as'
PostDelta: no visible global function definition for 'head'
PostDelta: no visible global function definition for 'as'
PostDup: no visible global function definition for 'head'
PostDup: no visible global function definition for 'as'
PostError: no visible global function definition for 'head'
PostError: no visible global function definition for 'summarySeg'
PostError: no visible global function definition for 'as'
PostSigma: no visible global function definition for 'head'
PostSigma: no visible global function definition for 'as'
RawReadsTrack: no visible global function definition for 'seqnames'
RawReadsTrack: no visible global function definition for 'start'
RawReadsTrack: no visible global function definition for 'end'
RawReadsTrack: no visible global function definition for 'strand'
make.thickthin: no visible global function definition for 'as.roman'
newPing: no visible global function definition for 'new'
newPingError: no visible global function definition for 'new'
newPingList: no visible global function definition for 'new'
postPING: no visible global function definition for 'as'
segmentPING: no visible global function definition for 'var'
segmentPING: no visible global function definition for 'seqlevels'
segmentPING: no visible global function definition for 'IRanges'
segmentPING: no visible global function definition for 'start'
segmentPING: no visible global function definition for 'end'
segmentPING: no visible global function definition for
  'candidate.region'
segmentPING: no visible global function definition for 'segChrRead'
segmentPING: no visible global function definition for 'segReadsListPE'
truncateResult: no visible global function definition for 'read.table'
as.data.frame,pingList: no visible global function definition for 'as'
plot,data.frame-data.frame: no visible global function definition for
  'pingFDR2'
plot,data.frame-data.frame: no visible global function definition for
  'tail'
plot,data.frame-data.frame: no visible global function definition for
  'head'
plot,ping-segReads : .densityMix: no visible global function definition
  for 'dt'
plot,ping-segReads: no visible global function definition for 'tail'
plot,pingError-segReads: no visible global function definition for
  'tail'
plot,pingList-pingList: no visible global function definition for
  'pingFDR'
show,pingList: no visible global function definition for 'getSlots'
summary,segReads: no visible global function definition for 'tail'
Undefined global functions or variables:
  IRanges as as.roman candidate.region coverage dt end getSlots head
  new pingFDR pingFDR2 quantile read.table resize segChrRead
  segReadsListPE seqlevels seqnames start strand summarySeg tail var
  width
Consider adding
  importFrom("methods", "as", "getSlots", "new")
  importFrom("stats", "dt", "end", "quantile", "start", "var")
  importFrom("utils", "as.roman", "head", "read.table", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'CoverageTrack' 'NucleosomeTrack' 'PING' 'RawReadsTrack'
  'makeGRangesOutput' 'newPing' 'newPingError' 'newPingList'
  'plotSummary' 'segmentPING'
Undocumented S4 classes:
  'ping' 'pingList' 'pingError'
Undocumented S4 methods:
  generic '[' and siglist 'pingList,ANY,ANY,ANY'
  generic 'as.data.frame' and siglist 'pingList'
  generic 'density' and siglist 'ping'
  generic 'density' and siglist 'pingError'
  generic 'density' and siglist 'pingList'
  generic 'plot' and siglist 'data.frame,data.frame'
  generic 'plot' and siglist 'ping,segReads'
  generic 'plot' and siglist 'pingError,segReads'
  generic 'plot' and siglist 'pingList,pingList'
  generic 'plot' and siglist 'pingList,segReadsList'
  generic 'show' and siglist 'pingList'
  generic 'summary' and siglist 'ping'
  generic 'summary' and siglist 'pingList'
  generic 'summary' and siglist 'segReads'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'postPING.Rd':
  ‘minK’ ‘maxK’ ‘tol’ ‘B’ ‘mSelect’ ‘mergePeaks’ ‘mapCorrect’ ‘xi’
  ‘rho’ ‘alpha’ ‘beta’ ‘lambda’ ‘dMu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ... OK
* 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-arm64/Resources/library/PING/libs/PING.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘PING.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... NONE
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PING.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PING
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘PING’ ...
** using staged installation
checking for pkg-config... /opt/R/arm64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ping.c -o ping.o
ping.c:145:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                          &&
ping.c:145:7: note: cast one or both operands to int to silence this warning
ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
         ^
ping.c:321:10: note: use function 'fabs' instead
      if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
         ^~~
         fabs
ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
         ^
ping.c:329:10: note: use function 'fabs' instead
      if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
         ^~~
         fabs
ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
           ^
ping.c:345:12: note: use function 'fabs' instead
        if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
           ^~~
           fabs
ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
           ^
ping.c:353:12: note: use function 'fabs' instead
        if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
           ^~~
           fabs
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
        double chiSum = 0, etaF, etaR, dd, cc;
               ^
ping.c:3408:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1))
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                             ||
ping.c:3408:10: note: cast one or both operands to int to silence this warning
ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
  double tstat=0.0,tstatMax=0.0;
                   ^
8 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PING.so init.o ping.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-PING/00new/PING/libs
** R
** 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 (PING)