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INSTALL report for LVSmiRNA on tokay2

This page was generated on 2018-10-17 08:34:58 -0400 (Wed, 17 Oct 2018).

Package 807/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LVSmiRNA 1.30.0
Stefano Calza
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/LVSmiRNA
Branch: RELEASE_3_7
Last Commit: 8ba7c8b
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: LVSmiRNA
Version: 1.30.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/LVSmiRNA_1.30.0.tar.gz && rm -rf LVSmiRNA.buildbin-libdir && mkdir LVSmiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LVSmiRNA.buildbin-libdir LVSmiRNA_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LVSmiRNA_1.30.0.zip && rm LVSmiRNA_1.30.0.tar.gz LVSmiRNA_1.30.0.zip
StartedAt: 2018-10-16 19:42:27 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:43:09 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 41.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/LVSmiRNA_1.30.0.tar.gz && rm -rf LVSmiRNA.buildbin-libdir && mkdir LVSmiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LVSmiRNA.buildbin-libdir LVSmiRNA_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LVSmiRNA_1.30.0.zip && rm LVSmiRNA_1.30.0.tar.gz LVSmiRNA_1.30.0.zip
###
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100  317k  100  317k    0     0  6033k      0 --:--:-- --:--:-- --:--:-- 6894k

install for i386

* installing *source* package 'LVSmiRNA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c basic_fns.c -o basic_fns.o
basic_fns.c: In function 'lvs_median':
basic_fns.c:146:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c: In function 'gamma_fit':
lvs_rlm.c:175:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
lvs_rlm.c: In function 'test_gamma_fit':
lvs_rlm.c:286:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o LVSmiRNA.dll tmp.def basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/LVSmiRNA.buildbin-libdir/LVSmiRNA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
** help
*** installing help indices
  converting help for package 'LVSmiRNA'
    finding HTML links ... done
    MIR-spike-in                            html  
    RLM                                     html  
    boxplot-methods                         html  
    estVC                                   html  
    exprs-methods                           html  
    exprs_assign-methods                    html  
    featureNames-method                     html  
    lvs                                     html  
    plotRA                                  html  
    finding level-2 HTML links ... done

    preproc-methods                         html  
    preproc_assign-methods                  html  
    probeNames-methods                      html  
    read.mir                                html  
    rlmFit                                  html  
    sampleNames-methods                     html  
    summarize                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
In R CMD INSTALL

install for x64

* installing *source* package 'LVSmiRNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c basic_fns.c -o basic_fns.o
basic_fns.c: In function 'lvs_median':
basic_fns.c:146:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c: In function 'gamma_fit':
lvs_rlm.c:175:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
lvs_rlm.c: In function 'test_gamma_fit':
lvs_rlm.c:286:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o LVSmiRNA.dll tmp.def basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/LVSmiRNA.buildbin-libdir/LVSmiRNA/libs/x64
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
* MD5 sums
packaged installation of 'LVSmiRNA' as LVSmiRNA_1.30.0.zip
* DONE (LVSmiRNA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'LVSmiRNA' successfully unpacked and MD5 sums checked
In R CMD INSTALL