Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

INSTALL report for ncdfFlow on tokay1

This page was generated on 2019-04-13 11:21:56 -0400 (Sat, 13 Apr 2019).

Package 1041/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.28.1
Mike Jiang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ncdfFlow
Branch: RELEASE_3_8
Last Commit: 5c7f7de
Last Changed Date: 2019-01-04 13:41:41 -0400 (Fri, 04 Jan 2019)
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: ncdfFlow
Version: 2.28.1
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ncdfFlow_2.28.1.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.28.1.zip && rm ncdfFlow_2.28.1.tar.gz ncdfFlow_2.28.1.zip
StartedAt: 2019-04-12 19:08:53 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:11:43 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ncdfFlow_2.28.1.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.28.1.zip && rm ncdfFlow_2.28.1.tar.gz ncdfFlow_2.28.1.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 55732  100 55732    0     0  1553k      0 --:--:-- --:--:-- --:--:-- 1755k

install for i386

* installing *source* package 'ncdfFlow' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bitOps.cpp -o bitOps.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hdfFlow.cpp -o hdfFlow.o
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:87:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned i = 0; i < j_val.size(); i++){
                          ^
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/i386/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/i386/libncdfFlow.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/i386 -lhdf5 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ncdfFlow'
    finding HTML links ... done
    Indices                                 html  
    as.flowSet                              html  
    clone.ncdfFlowSet                       html  
    extractFlowFrame                        html  
    finding level-2 HTML links ... done

    flowSet-accessor                        html  
    getFileName                             html  
    lapply-methods                          html  
    ncdfFlow                                html  
    ncdfFlowList-class                      html  
    ncdfFlowSet-Subset                      html  
    ncdfFlowSet-class                       html  
    ncdfFlowSet-constructor                 html  
    ncdfFlowSet-split                       html  
    ncfsApply-ncdfFlowSet-method            html  
    plot                                    html  
    rbind2-method                           html  
    read.ncdfFlowSet                        html  
    replacement-method-for-ncdfFlowSet      html  
    save_ncfs                               html  
    subset-functions                        html  
    subset-methods                          html  
    unlink-ncdfFlowSet-method               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ncdfFlow' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bitOps.cpp -o bitOps.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hdfFlow.cpp -o hdfFlow.o
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readFrame.cpp -o readFrame.o
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/x64 -lhdf5 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.28.1.zip
* DONE (ncdfFlow)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ncdfFlow' successfully unpacked and MD5 sums checked
In R CMD INSTALL