Package: PING

Version: 2.28.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PING.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PING_2.28.0.tar.gz

StartedAt: 2019-10-16 06:00:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:07:48 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 468.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PING.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PING.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PING_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.28.0'
* 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:
  ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ping.c:912:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ping.c:1072:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ping.c:1320:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ping.c:1473:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/CoverageTrack.Rd:32: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:21: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:34: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:35: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/RawReadsTrack.Rd:33: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
    libs      1.4Mb
* 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
* 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 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 : : 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 ... 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, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PING_2.28.0.tar.gz && rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PING.buildbin-libdir PING_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PING_2.28.0.zip && rm PING_2.28.0.tar.gz PING_2.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5127k  100 5127k    0     0  42.8M      0 --:--:-- --:--:-- --:--:-- 45.9M

install for i386

* installing *source* package 'PING' ...
** using staged installation

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include    -I"C:/extsoft/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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include    -I"C:/extsoft/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/gcc -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/PING.buildbin-libdir/00LOCK-PING/00new/PING/libs/i386
** R
** inst
** byte-compile and prepare 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-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/CoverageTrack.Rd:32: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
    NucleosomeTrack                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:21: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:34: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/NucleosomeTrack.Rd:35: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
    PICS_IMPORT                             html  
    PING                                    html  
    RawReadsTrack                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCo3NbN/R.INSTALL24d4734879a1/PING/man/RawReadsTrack.Rd:33: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
    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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/extsoft/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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/extsoft/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/gcc -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/PING.buildbin-libdir/PING/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PING' as PING_2.28.0.zip
* DONE (PING)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PING' successfully unpacked and MD5 sums checked