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INSTALL report for PING on tokay2

This page was generated on 2019-04-09 12:00:20 -0400 (Tue, 09 Apr 2019).

Package 1191/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.27.0
Renan Sauteraud
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/PING
Branch: master
Last Commit: e4566a1
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: PING
Version: 2.27.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PING_2.27.0.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_2.27.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PING_2.27.0.zip && rm PING_2.27.0.tar.gz PING_2.27.0.zip
StartedAt: 2019-04-08 20:35:00 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:36:56 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 116.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PING_2.27.0.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_2.27.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PING_2.27.0.zip && rm PING_2.27.0.tar.gz PING_2.27.0.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  22.2M      0 --:--:-- --:--:-- --:--:-- 22.9M

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˜1.9-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/Rtmpqap6eQ/R.INSTALL25fc54fe64e0/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/Rtmpqap6eQ/R.INSTALL25fc54fe64e0/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/Rtmpqap6eQ/R.INSTALL25fc54fe64e0/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/Rtmpqap6eQ/R.INSTALL25fc54fe64e0/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/Rtmpqap6eQ/R.INSTALL25fc54fe64e0/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_2.27.0.zip
* DONE (PING)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PING' successfully unpacked and MD5 sums checked