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INSTALL report for batchelor on tokay2

This page was generated on 2020-10-17 11:56:07 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE batchelor PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 119/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
batchelor 1.4.0
Aaron Lun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/batchelor
Branch: RELEASE_3_11
Last Commit: cfce683
Last Changed Date: 2020-04-27 15:25:15 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: batchelor
Version: 1.4.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/batchelor_1.4.0.tar.gz && rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL batchelor_1.4.0.zip && rm batchelor_1.4.0.tar.gz batchelor_1.4.0.zip
StartedAt: 2020-10-16 18:35:29 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:37:39 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 130.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/batchelor_1.4.0.tar.gz && rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL batchelor_1.4.0.zip && rm batchelor_1.4.0.tar.gz batchelor_1.4.0.zip
###
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100  108k  100  108k    0     0   624k      0 --:--:-- --:--:-- --:--:--  648k

install for i386

* installing *source* package 'batchelor' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'Rcpp::NumericVector adjust_shift_variance(Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, double, Rcpp::IntegerVector, Rcpp::IntegerVector)':
adjust_shift_variance.cpp:131:39: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
             for (size_t other=0; other<restrict1.size(); ++other) {
                                  ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c find_mutual_nns.cpp -o find_mutual_nns.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::RObject, double)':
smooth_gaussian_kernel.cpp:21:13: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     if (nmnn!=index.size()) {
         ~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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  
    batchelor-restrict                      html  
    checkInputs                             html  
    clusterMNN                              html  
    correctExperiments                      html  
    cosineNorm                              html  
    divideIntoBatches                       html  
    fastMNN                                 html  
    findMutualNN                            html  
    mnnCorrect                              html  
    multiBatchNorm                          html  
    multiBatchPCA                           html  
    noCorrect                               html  
    reducedMNN                              html  
    regressBatches                          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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'Rcpp::NumericVector adjust_shift_variance(Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, double, Rcpp::IntegerVector, Rcpp::IntegerVector)':
adjust_shift_variance.cpp:131:39: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
             for (size_t other=0; other<restrict1.size(); ++other) {
                                  ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c find_mutual_nns.cpp -o find_mutual_nns.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::RObject, double)':
smooth_gaussian_kernel.cpp:21:13: 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 (nmnn!=index.size()) {
         ~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/batchelor.buildbin-libdir/batchelor/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'batchelor' as batchelor_1.4.0.zip
* DONE (batchelor)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'batchelor' successfully unpacked and MD5 sums checked