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CHECK report for PING on tokay1

This page was generated on 2018-04-12 13:21:36 -0400 (Thu, 12 Apr 2018).

Package 1041/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.22.0
Renan Sauteraud
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PING
Branch: RELEASE_3_6
Last Commit: bb40490
Last Changed Date: 2017-10-30 12:39:38 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: PING
Version: 2.22.0
Command: rm -rf PING.buildbin-libdir PING.Rcheck && mkdir PING.buildbin-libdir PING.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PING.buildbin-libdir PING_2.22.0.tar.gz >PING.Rcheck\00install.out 2>&1 && cp PING.Rcheck\00install.out PING-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PING.buildbin-libdir --install="check:PING-install.out" --force-multiarch --no-vignettes --timings PING_2.22.0.tar.gz
StartedAt: 2018-04-12 02:10:24 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:17:16 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 412.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: PING.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PING.buildbin-libdir PING.Rcheck && mkdir PING.buildbin-libdir PING.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PING.buildbin-libdir PING_2.22.0.tar.gz >PING.Rcheck\00install.out 2>&1 && cp PING.Rcheck\00install.out PING-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PING.buildbin-libdir --install="check:PING-install.out" --force-multiarch --no-vignettes --timings PING_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PING/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PING' version '2.22.0'
* 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 whether package 'PING' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/CoverageTrack.Rd:32: missing file link 'AnnotationTrack'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:21: missing file link 'AnnotationTrack'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:34: missing file link 'DataTrack'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:35: missing file link 'AnnotationTrack'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/RawReadsTrack.Rd:33: missing file link 'DataTrack'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
    libs      1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'IRanges'
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
* loading checks for arch 'i386'
** 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: 'density'

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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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: 'density'

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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BSgenome' 'BiocGenerics' 'fda' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GenomicRanges' 'chipseq'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'parallel:::detectCores' 'parallel:::makeCluster'
  'parallel:::parLapply' 'parallel:::stopCluster'
  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
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 'seqnames'
FilterPING: no visible global function definition for 'density'
NucleosomeTrack: no visible global function definition for 'as'
PostDelta: no visible global function definition for 'as'
PostDup: no visible global function definition for 'as'
PostError: no visible global function definition for 'as'
PostSigma: no visible global function definition for 'as'
RawReadsTrack: no visible global function definition for 'seqnames'
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 'seqlevels'
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,ping-segReads: no visible global function definition for 'density'
plot,pingError-segReads: no visible global function definition for
  'density'
plot,pingList-pingList: no visible global function definition for
  'pingFDR'
show,pingList: no visible global function definition for 'getSlots'
Undefined global functions or variables:
  as as.roman density getSlots new pingFDR pingFDR2 read.table
  seqlevels seqnames strand
Consider adding
  importFrom("methods", "as", "getSlots", "new")
  importFrom("stats", "density")
  importFrom("utils", "as.roman", "read.table")
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 S4 methods:
  generic '[' and siglist 'pingList,ANY,ANY,ANY'
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 ... OK
* 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 ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.buildbin-libdir/PING/libs/i386/PING.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 WARNINGs, 8 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.Rcheck/00check.log'
for details.



Installation output

PING.Rcheck/00install.out


install for i386

* installing *source* package 'PING' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   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: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
  double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
                         ^
ping.c: In function 'ECM1':
ping.c:912:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1072:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:760:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
ping.c: In function 'ECM1PE':
ping.c:1320:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1473:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
         ^
ping.c:1527:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                                ^
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                         ^
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
   double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR; 
                                                           ^
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
   double tstat=0.0,tstatMax=0.0;
                    ^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
           ^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
       ^
ping.c: In function 'BIC':
ping.c:2101:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
      ^
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
      ^
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans, temp, firstFit;
                  ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.buildbin-libdir/PING/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'PING'
    finding HTML links ... done
    CoverageTrack                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/CoverageTrack.Rd:32: missing file link 'AnnotationTrack'
    NucleosomeTrack                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:21: missing file link 'AnnotationTrack'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:34: missing file link 'DataTrack'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:35: missing file link 'AnnotationTrack'
    PICS_IMPORT                             html  
    PING                                    html  
    RawReadsTrack                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/RawReadsTrack.Rd:33: missing file link 'DataTrack'
    ping-class                              html  
    pingError-class                         html  
    pingList-class                          html  
    plotSummary                             html  
    postPING                                html  
    segmentPING                             html  
    show                                    html  
    summary                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PING' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   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: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
  double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
                         ^
ping.c: In function 'ECM1':
ping.c:912:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1072:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:760:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
ping.c: In function 'ECM1PE':
ping.c:1320:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1473:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
         ^
ping.c:1527:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                                ^
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                         ^
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
   double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR; 
                                                           ^
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
   double tstat=0.0,tstatMax=0.0;
                    ^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
           ^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
       ^
ping.c: In function 'BIC':
ping.c:2101:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
      ^
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
      ^
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans, temp, firstFit;
                  ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.buildbin-libdir/PING/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PING' as PING_2.22.0.zip
* DONE (PING)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

PING.Rcheck/examples_i386/PING-Ex.timings

nameusersystemelapsed
ping-class000
pingError-class0.020.000.02
pingList-class000
segmentPING0.450.050.50

PING.Rcheck/examples_x64/PING-Ex.timings

nameusersystemelapsed
ping-class000
pingError-class000
pingList-class000
segmentPING1.210.001.27