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BUILD BIN report for batchelor on tokay2

This page was generated on 2019-04-09 12:45:56 -0400 (Tue, 09 Apr 2019).

Package 107/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
batchelor 0.99.7
Aaron Lun
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/batchelor
Branch: master
Last Commit: 4ff6842
Last Changed Date: 2019-03-27 00:58:14 -0400 (Wed, 27 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: batchelor
Version: 0.99.7
Command: rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_0.99.7.tar.gz
StartedAt: 2019-04-09 07:28:11 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 07:30:30 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 138.8 seconds
RetCode: 0
Status:  OK  
PackageFile: batchelor_0.99.7.zip
PackageFileSize: 1.54 MiB

Command output

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###
### Running command:
###
###   rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_0.99.7.tar.gz
###
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install for i386

* installing *source* package 'batchelor' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
adjust_shift_variance.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t other=0; other<restricted1.size(); ++other) {
                                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cosine_norm.cpp -o cosine_norm.o
In file included from cosine_norm.cpp:6:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47:   required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]'
cosine_norm.cpp:70:79:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47:   required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]'
cosine_norm.cpp:72:79:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
smooth_gaussian_kernel.cpp:20:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) { 
               ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c unlog_exprs.cpp -o unlog_exprs.o
unlog_exprs.cpp: In function 'SEXPREC* unlog_exprs_scaled(SEXP, SEXP, SEXP, SEXP, SEXP)':
unlog_exprs.cpp:51:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (slen!=rescaling.size()) {
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:9:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (isNA(s) || s < 0 || s >= len) {
                                   ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/batchelor.buildbin-libdir/00LOCK-batchelor/00new/batchelor/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'batchelor'
    finding HTML links ... done
    BatchelorParam                          html  
    finding level-2 HTML links ... done

    batchCorrect                            html  
    checkInputs                             html  
    cosineNorm                              html  
    divideIntoBatches                       html  
    fastMNN                                 html  
    findMutualNN                            html  
    mnnCorrect                              html  
    multiBatchNorm                          html  
    multiBatchPCA                           html  
    rescaleBatches                          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 'batchelor' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
adjust_shift_variance.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t other=0; other<restricted1.size(); ++other) {
                                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cosine_norm.cpp -o cosine_norm.o
In file included from cosine_norm.cpp:6:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47:   required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]'
cosine_norm.cpp:70:79:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47:   required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]'
cosine_norm.cpp:72:79:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
smooth_gaussian_kernel.cpp:20:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) { 
               ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c unlog_exprs.cpp -o unlog_exprs.o
unlog_exprs.cpp: In function 'SEXPREC* unlog_exprs_scaled(SEXP, SEXP, SEXP, SEXP, SEXP)':
unlog_exprs.cpp:51:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (slen!=rescaling.size()) {
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:9:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (isNA(s) || s < 0 || s >= len) {
                                   ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/batchelor.buildbin-libdir/batchelor/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'batchelor' as batchelor_0.99.7.zip
* DONE (batchelor)