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CHECK report for csaw on tokay1

This page was generated on 2019-04-13 11:24:32 -0400 (Sat, 13 Apr 2019).

Package 350/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.16.1
Aaron Lun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/csaw
Branch: RELEASE_3_8
Last Commit: 63ef4a6
Last Changed Date: 2018-12-20 19:32:06 -0400 (Thu, 20 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: csaw
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:csaw.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings csaw_1.16.1.tar.gz
StartedAt: 2019-04-13 01:35:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:48:25 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 803.8 seconds
RetCode: 0
Status:  OK  
CheckDir: csaw.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:csaw.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings csaw_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/csaw.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'csaw/DESCRIPTION' ... OK
* this is package 'csaw' version '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'csaw' can be installed ... 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
* 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 ... OK
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking 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-3.8-bioc/R/library/csaw/libs/i386/csaw.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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
Examples with CPU or elapsed time > 5s
             user system elapsed
detailRanges 8.39   0.53    9.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
detailRanges 6.63   0.16    6.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/csaw.Rcheck/00check.log'
for details.

Installation output

csaw.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/csaw_1.16.1.tar.gz && rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=csaw.buildbin-libdir csaw_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL csaw_1.16.1.zip && rm csaw_1.16.1.tar.gz csaw_1.16.1.zip
###
##############################################################################
##############################################################################


  % 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  901k  100  901k    0     0  20.4M      0 --:--:-- --:--:-- --:--:-- 22.5M

install for i386

* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c annotator.cpp -o annotator.o
annotator.cpp: In function 'SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
annotator.cpp:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (counter < nolaps && query[counter]==curreg) { 
                        ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function 'SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)':
best_in_cluster.cpp:11:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
          ^
best_in_cluster.cpp:11:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
                                   ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_maxima.cpp -o find_maxima.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In function 'SEXPREC* get_cluster_stats(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_cluster_stats.cpp:17:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (nwin!=current.size()) { 
           ^
get_cluster_stats.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (clustid.size()!=nwin) {
                       ^
get_cluster_stats.cpp:33:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=winweight.size()) { 
          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'csaw'
    finding HTML links ... done
    SEmethods                               html  
    finding level-2 HTML links ... done

    calculateCPM                            html  
    checkBimodality                         html  
    clusterFDR                              html  
    clusterWindows                          html  
    combineTests                            html  
    consolidateClusters                     html  
    consolidateTests                        html  
    consolidateWindows                      html  
    correlateReads                          html  
    csawUsersGuide                          html  
    detailRanges                            html  
    empiricalFDR                            html  
    extractReads                            html  
    filterWindows                           html  
    findMaxima                              html  
    getBestTest                             html  
    getPESizes                              html  
    getWidths                               html  
    maximizeCcf                             html  
    mergeWindows                            html  
    mixedClusters                           html  
    normOffsets                             html  
    overlapStats                            html  
    profileSites                            html  
    readParam                               html  
    regionCounts                            html  
    scaledAverage                           html  
    strandedCounts                          html  
    upweightSummit                          html  
    windowCounts                            html  
    wwhm                                    html  
** building package indices
** installing vignettes
   'csaw.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c annotator.cpp -o annotator.o
annotator.cpp: In function 'SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
annotator.cpp:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (counter < nolaps && query[counter]==curreg) { 
                        ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function 'SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)':
best_in_cluster.cpp:11:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
          ^
best_in_cluster.cpp:11:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
                                   ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_maxima.cpp -o find_maxima.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In function 'SEXPREC* get_cluster_stats(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_cluster_stats.cpp:17:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (nwin!=current.size()) { 
           ^
get_cluster_stats.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (clustid.size()!=nwin) {
                       ^
get_cluster_stats.cpp:33:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=winweight.size()) { 
          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.16.1.zip
* DONE (csaw)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'csaw' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

csaw.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(csaw)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("csaw")
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen]== testthat results  ===========================================================
OK: 2687 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
 211.32    3.79  215.87 
 SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.

csaw.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(csaw)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("csaw")
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen]== testthat results  ===========================================================
OK: 2687 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
 216.43    2.57  219.31 
 SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.

Example timings

csaw.Rcheck/examples_i386/csaw-Ex.timings

nameusersystemelapsed
SEmethods0.430.000.64
calculateCPM0.360.000.36
checkBimodality0.330.030.35
clusterFDR0.920.000.93
clusterWindows1.440.001.43
combineTests0.120.020.14
consolidateClusters3.330.003.33
consolidateTests0.750.020.77
consolidateWindows0.420.000.43
correlateReads0.280.000.28
csawUsersGuide0.020.000.01
detailRanges8.390.539.08
empiricalFDR0.060.000.06
extractReads0.670.050.72
filterWindows0.480.190.67
findMaxima0.100.000.09
getBestTest0.040.000.05
getPESizes0.110.000.11
getWidths0.520.000.52
maximizeCcf0.020.000.01
mergeWindows0.040.000.05
mixedClusters0.100.000.09
normOffsets0.120.000.13
overlapStats0.580.000.57
profileSites0.700.000.71
readParam0.030.000.03
regionCounts0.380.000.37
scaledAverage0.480.000.49
strandedCounts1.410.001.40
upweightSummit0.010.000.02
windowCounts0.680.000.67
wwhm0.060.000.06

csaw.Rcheck/examples_x64/csaw-Ex.timings

nameusersystemelapsed
SEmethods0.320.000.43
calculateCPM0.840.000.84
checkBimodality0.270.000.33
clusterFDR0.680.090.78
clusterWindows1.390.021.40
combineTests0.100.020.11
consolidateClusters2.140.002.14
consolidateTests0.420.000.43
consolidateWindows0.390.000.39
correlateReads0.140.010.81
csawUsersGuide000
detailRanges6.630.166.83
empiricalFDR0.060.000.07
extractReads1.070.001.06
filterWindows0.790.000.80
findMaxima0.180.000.17
getBestTest0.080.000.08
getPESizes0.160.000.16
getWidths0.40.00.4
maximizeCcf0.020.000.02
mergeWindows0.030.000.03
mixedClusters0.060.000.06
normOffsets0.080.000.08
overlapStats0.440.000.44
profileSites0.530.000.53
readParam0.030.000.03
regionCounts0.220.010.24
scaledAverage0.340.020.35
strandedCounts1.390.001.40
upweightSummit000
windowCounts0.750.000.75
wwhm0.080.000.07