Back to Multiple platform build/check report for BioC 3.7
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

INSTALL report for genoCN on tokay2

This page was generated on 2018-10-17 08:34:39 -0400 (Wed, 17 Oct 2018).

Package 585/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.32.0
Wei Sun
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/genoCN
Branch: RELEASE_3_7
Last Commit: a2de30a
Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.32.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/genoCN_1.32.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL genoCN_1.32.0.zip && rm genoCN_1.32.0.tar.gz genoCN_1.32.0.zip
StartedAt: 2018-10-16 18:34:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:34:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 43.5 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/genoCN_1.32.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL genoCN_1.32.0.zip && rm genoCN_1.32.0.tar.gz genoCN_1.32.0.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  739k  100  739k    0     0  11.4M      0 --:--:-- --:--:-- --:--:-- 12.8M

install for i386

* installing *source* package 'genoCN' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c tnorm_mle.c -o tnorm_mle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utility.c -o utility.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
                    ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
          ^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
          ^
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/genoCN.buildbin-libdir/genoCN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genoCN'
    finding HTML links ... done
    code.genotype                           html  
    genoCNA                                 html  
    genoCNV                                 html  
    init.Para.CNA                           html  
    init.Para.CNV                           html  
    plotCN                                  html  
    snpData                                 html  
    snpInfo                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genoCN' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tnorm_mle.c -o tnorm_mle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utility.c -o utility.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
                    ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
          ^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
          ^
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/genoCN.buildbin-libdir/genoCN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoCN' as genoCN_1.32.0.zip
* DONE (genoCN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'genoCN' successfully unpacked and MD5 sums checked
In R CMD INSTALL