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BioC 2.14: CHECK report for CSSP on morelia

This page was generated on 2014-10-08 09:06:36 -0700 (Wed, 08 Oct 2014).

Package 201/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.2.0
Chandler Zuo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CSSP
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: CSSP
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CSSP_1.2.0.tar.gz
StartedAt: 2014-10-07 22:16:12 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:17:10 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 58.1 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CSSP.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CSSP_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CSSP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CSSP’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 R 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’ ‘utils’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
cssp.power-methods 24.502  0.177  24.857
cssp.fit-methods    6.069  0.046   6.127
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_tests.R’ [4s/4s]
 ERROR
Running the tests in ‘tests/run_tests.R’ failed.
Last 13 lines of output:
  chromosomes in GC contains chr1
  chromosomes in N contains 
  chiptag contains 201 bins for chromosome chr1
  Read in values for 201 bins for chromosome chr1
  .......
  
  
  1. Failure(@test-cssp.fit.R#29): Function cssp.fit: check the data.frame and BinData data formats are equivalent 
  fit1@a not equal to fit2@a
  Mean relative difference: 0.1
  
  Error: Test failures
  Execution halted

CSSP.Rcheck/00install.out:

* installing *source* package ‘CSSP’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c bincount.c -o bincount.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c binpower.c -o binpower.o
binpower.c:86:5: warning: variable 'p_thre' is uninitialized when used here [-Wuninitialized]
    p_thre+=compute_p(sim_bin,n,0.05);
    ^˜˜˜˜˜
binpower.c:56:48: note: initialize the variable 'p_thre' to silence this warning
  double sim_bin[n],tmpcount,tmp,tmprate,p_thre,ptail_sig[ncomp],rej_back,binpow;
                                               ^
                                                = 0.0
binpower.c:141:10: warning: unused variable 'sim_bin' [-Wunused-variable]
  double sim_bin[n],tmpcount,tmp,tmprate,ptail_sig[ncomp],rej_back,binpow;
         ^
binpower.c:136:11: warning: unused variable 'rsize_back' [-Wunused-variable]
  double *rsize_back=REAL(size_back), *rscale_back=REAL(scale_back), *rscale_sig=REAL(scale_sig), *rsize_sig=REAL(size_sig), *rprob_bind=REAL(prob_bind), *rprob_sig=REAL(prob_sig), *rprob_zero=REAL(prob_zero);
          ^
binpower.c:141:30: warning: unused variable 'tmp' [-Wunused-variable]
  double sim_bin[n],tmpcount,tmp,tmprate,ptail_sig[ncomp],rej_back,binpow;
                             ^
binpower.c:136:40: warning: unused variable 'rscale_back' [-Wunused-variable]
  double *rsize_back=REAL(size_back), *rscale_back=REAL(scale_back), *rscale_sig=REAL(scale_sig), *rsize_sig=REAL(size_sig), *rprob_bind=REAL(prob_bind), *rprob_sig=REAL(prob_sig), *rprob_zero=REAL(prob_zero);
                                       ^
binpower.c:135:34: warning: unused variable 'k' [-Wunused-variable]
  R_len_t n= length(mu_chip),i,j,k,isig,nite=REAL(ite)[0],ncomp=length(size_sig)/length(mu_chip);
                                 ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridLogMean.c -o gridLogMean.o
gridLogMean.c:29:75: warning: | has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gridLogMean.c:29:75: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
                                                                            (                      )
gridLogMean.c:29:75: note: place parentheses around the | expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
             (                                                                     )
gridLogMean.c:29:130: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^˜˜˜˜˜
gridLogMean.c:29:130: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
                                                                                                                                  (    )
gridLogMean.c:29:130: note: place parentheses around the & expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
            (                                                                                                                      )
gridLogMean.c:35:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridLogMean.c:35:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridLogMean.c:35:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
gridLogMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                              ^
gridLogMean.c:193:69: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^˜˜˜˜˜
gridLogMean.c:193:69: note: place parentheses around the '<' expression to silence this warning
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
                                                                     (    )
gridLogMean.c:193:69: note: place parentheses around the & expression to evaluate it first
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
            (                                                         )
gridLogMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                              ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridMGC.c -o gridMGC.o
gridMGC.c:29:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridMGC.c:29:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridMGC.c:29:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridMean.c -o gridMean.o
gridMean.c:29:75: warning: | has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gridMean.c:29:75: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
                                                                            (                      )
gridMean.c:29:75: note: place parentheses around the | expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
             (                                                                     )
gridMean.c:29:130: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^˜˜˜˜˜
gridMean.c:29:130: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
                                                                                                                                  (    )
gridMean.c:29:130: note: place parentheses around the & expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
            (                                                                                                                      )
gridMean.c:35:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridMean.c:35:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridMean.c:35:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                              ^
gridMean.c:193:69: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^˜˜˜˜˜
gridMean.c:193:69: note: place parentheses around the '<' expression to silence this warning
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
                                                                     (    )
gridMean.c:193:69: note: place parentheses around the & expression to evaluate it first
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
            (                                                         )
gridMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                              ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridMode.c -o gridMode.o
gridMode.c:31:75: warning: | has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gridMode.c:31:75: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
                                                                            (                      )
gridMode.c:31:75: note: place parentheses around the | expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
             (                                                                     )
gridMode.c:31:130: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^˜˜˜˜˜
gridMode.c:31:130: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
                                                                                                                                  (    )
gridMode.c:31:130: note: place parentheses around the & expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
            (                                                                                                                      )
gridMode.c:37:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridMode.c:37:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridMode.c:37:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
gridMode.c:219:69: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^˜˜˜˜˜
gridMode.c:219:69: note: place parentheses around the '<' expression to silence this warning
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
                                                                     (    )
gridMode.c:219:69: note: place parentheses around the & expression to evaluate it first
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
            (                                                         )
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridNonpa.c -o gridNonpa.o
gridNonpa.c:29:75: warning: | has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gridNonpa.c:29:75: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
                                                                            (                      )
gridNonpa.c:29:75: note: place parentheses around the | expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
             (                                                                     )
gridNonpa.c:29:130: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^˜˜˜˜˜
gridNonpa.c:29:130: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
                                                                                                                                  (    )
gridNonpa.c:29:130: note: place parentheses around the & expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
            (                                                                                                                      )
gridNonpa.c:35:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridNonpa.c:35:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridNonpa.c:35:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
gridNonpa.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                              ^
gridNonpa.c:209:69: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^˜˜˜˜˜
gridNonpa.c:209:69: note: place parentheses around the '<' expression to silence this warning
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
                                                                     (    )
gridNonpa.c:209:69: note: place parentheses around the & expression to evaluate it first
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
            (                                                         )
gridNonpa.c:193:62: warning: unused variable 'counter' [-Wunused-variable]
        R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                                    ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gridSample.c -o gridSample.o
gridSample.c:33:75: warning: | has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gridSample.c:33:75: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
                                                                            (                      )
gridSample.c:33:75: note: place parentheses around the | expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                          ^
             (                                                                     )
gridSample.c:33:130: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^˜˜˜˜˜
gridSample.c:33:130: note: place parentheses around the '<' expression to silence this warning
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
                                                                                                                                  (    )
gridSample.c:33:130: note: place parentheses around the & expression to evaluate it first
      while(((Mgrid_u[l]<=Mgrid_l[l]+0.01 & GCgrid_u[l]>GCgrid_l[l]+0.01) | Mgrid_u[l]+Mgrid_l[l]<0 | GCgrid_u[l]+GCgrid_l[l]<0 )&l<k-1)
                                                                                                                                 ^
            (                                                                                                                      )
gridSample.c:39:25: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
gridSample.c:39:25: note: place parentheses around the '>' expression to silence this warning
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
             (                )
gridSample.c:39:25: note: place parentheses around the & expression to evaluate it first
          if(Ngrid[i]>Ngrid[l] & (Mgrid_u[i]>Mgrid_l[i]+0.01 | GCgrid_u[i]>GCgrid_l[i]+0.01) & Mgrid_u[l]+Mgrid_l[l]>0 & GCgrid_u[l]+GCgrid_l[l]>0)
                               ^
                      (                                                                     )
gridSample.c:224:69: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^˜˜˜˜˜
gridSample.c:224:69: note: place parentheses around the '<' expression to silence this warning
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
                                                                     (    )
gridSample.c:224:69: note: place parentheses around the & expression to evaluate it first
      while((Mgrid_u[l]<=Mgrid_l[l]+0.001 | Mgrid_u[l]+Mgrid_l[l]<0)&l<k-1)
                                                                    ^
            (                                                         )
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c tag2bin.c -o tag2bin.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/CSSP.Rcheck/CSSP/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CSSP)

CSSP.Rcheck/CSSP-Ex.timings:

nameusersystemelapsed
CSSPFit-class0.0030.0010.003
bindcount0.1280.0050.134
bindcount.chr0.0190.0010.020
callpeak-methods0.0130.0010.015
createBinData0.3850.0170.402
cssp.fit-methods6.0690.0466.127
cssp.power-methods24.502 0.17724.857
cssp.sim-methods0.0220.0090.031
fit.freq-methods0.2570.0090.267
pBBT-methods0.0060.0000.007
peakcount0.0990.0040.103
peakcount.chr0.0130.0010.013
qBBT-methods0.0310.0000.031
readBinFile0.0160.0020.019
tag2bin0.0090.0030.013
tag2bin.chr0.0050.0010.006