Back to "Blame Jeroen" build/check report for BioC 3.11

BUILD BIN report for csaw on tokay2

This page was generated on 2020-04-15 03:20:14 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE csaw PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 24/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.21.4
Aaron Lun
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/csaw
Branch: master
Last Commit: 60edc21
Last Changed Date: 2020-02-29 00:05:54 -0400 (Sat, 29 Feb 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]

Summary

Package: csaw
Version: 1.21.4
Command: rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=csaw.buildbin-libdir csaw_1.21.4.tar.gz
StartedAt: 2020-04-15 00:06:13 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:10:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 253.9 seconds
RetCode: 0
Status:  OK  
PackageFile: csaw_1.21.4.zip
PackageFileSize: 3.945 MiB

Command output

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### Running command:
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###   rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=csaw.buildbin-libdir csaw_1.21.4.tar.gz
###
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install for i386

* installing *source* package 'csaw' ...
** using staged installation
** libs
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
         while (counter < nolaps && query[counter]==curreg) {
                ~~~~~~~~^~~~~~~~
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bam_utils.cpp -o bam_utils.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:35: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
                               ~~~~^~~~~~~~~~~~~~~~~~
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c check_bimodality.cpp -o check_bimodality.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c correlate_reads.cpp -o correlate_reads.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c find_maxima.cpp -o find_maxima.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = SimesPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:266:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = HolmPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:276:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = MaxedPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:283:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_profile.cpp -o get_profile.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_rle_counts.cpp -o get_rle_counts.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c intersector.cpp -o intersector.o
intersector.cpp: In constructor 'intersector::intersector(SEXP, SEXP)':
intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     if (N!=elements.size()) {
         ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
         if (current < 0 || current >= nelements) {
                            ~~~~~~~~^~~~~~~~~~~~
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c merge_windows.cpp -o merge_windows.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pair_reads.cpp -o pair_reads.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c single_reads.cpp -o single_reads.o
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
/mingw32/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 intersector.o merge_windows.o pair_reads.o single_reads.o utils.o C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/csaw.buildbin-libdir/00LOCK-csaw/00new/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  
    cluster-direction                       html  
    clusterFDR                              html  
    clusterWindows                          html  
    clusterWindowsList                      html  
    combineTests                            html  
    correlateReads                          html  
    csawUsersGuide                          html  
    defunct                                 html  
    detailRanges                            html  
    empiricalFDR                            html  
    extractReads                            html  
    filterWindows                           html  
    findMaxima                              html  
    getBestTest                             html  
    getPESizes                              html  
    getWidths                               html  
    maximizeCcf                             html  
    mergeResults                            html  
    mergeResultsList                        html  
    mergeWindows                            html  
    mergeWindowsList                        html  
    minimalTests                            html  
    mixedTests                              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
** 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 'csaw' ...
** libs
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
         while (counter < nolaps && query[counter]==curreg) {
                ~~~~~~~~^~~~~~~~
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bam_utils.cpp -o bam_utils.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:35: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
                               ~~~~^~~~~~~~~~~~~~~~~~
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c check_bimodality.cpp -o check_bimodality.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c correlate_reads.cpp -o correlate_reads.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c find_maxima.cpp -o find_maxima.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = SimesPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:266:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = HolmPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:276:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
get_cluster_stats.cpp: In instantiation of 'SEXPREC* get_cluster_stats_internal(SEXP, SEXP, SEXP, SEXP, SEXP, PREP&) [with PREP = MaxedPreparer; SEXP = SEXPREC*]':
get_cluster_stats.cpp:283:80:   required from here
get_cluster_stats.cpp:172:11: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:183:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:188:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_profile.cpp -o get_profile.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c get_rle_counts.cpp -o get_rle_counts.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c intersector.cpp -o intersector.o
intersector.cpp: In constructor 'intersector::intersector(SEXP, SEXP)':
intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     if (N!=elements.size()) {
         ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
         if (current < 0 || current >= nelements) {
                            ~~~~~~~~^~~~~~~~~~~~
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c merge_windows.cpp -o merge_windows.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pair_reads.cpp -o pair_reads.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c single_reads.cpp -o single_reads.o
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
/mingw64/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 intersector.o merge_windows.o pair_reads.o single_reads.o utils.o C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.21.4.zip
* DONE (csaw)