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INSTALL report for CGEN on tokay2

This page was generated on 2018-10-17 08:34:52 -0400 (Wed, 17 Oct 2018).

Package 212/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.16.0
William Wheeler
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CGEN
Branch: RELEASE_3_7
Last Commit: 2702e09
Last Changed Date: 2018-04-30 10:35:14 -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: CGEN
Version: 3.16.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CGEN_3.16.0.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CGEN_3.16.0.zip && rm CGEN_3.16.0.tar.gz CGEN_3.16.0.zip
StartedAt: 2018-10-16 19:06:33 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:07:47 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 74.9 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/CGEN_3.16.0.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CGEN_3.16.0.zip && rm CGEN_3.16.0.tar.gz CGEN_3.16.0.zip
###
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100  635k  100  635k    0     0  9400k      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* installing *source* package 'CGEN' ...
** 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 Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
                   ^
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
                         ^
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 CML.c -o CML.o
CML.c:132:13: warning: 'print_dVec' defined but not used [-Wunused-function]
 static void print_dVec(vec, n, name)
             ^
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 ccl.c -o ccl.o
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c csclust.f -o csclust.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 fsclust.c -o fsclust.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 hcl.c -o hcl.o
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^
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 pmatch.c -o pmatch.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 score.c -o score.o
score.c: In function 'infoSmallStandard':
score.c:18:27: warning: unused variable 'ii' [-Wunused-variable]
   int  nr, nc, i, j, row, ii, nc2;
                           ^
score.c: In function 'getScoreEB':
score.c:183:21: warning: unused variable 'p6' [-Wunused-variable]
   double *p4, *p5, *p6;
                     ^
score.c:183:16: warning: unused variable 'p5' [-Wunused-variable]
   double *p4, *p5, *p6;
                ^
score.c:183:11: warning: unused variable 'p4' [-Wunused-variable]
   double *p4, *p5, *p6;
           ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CGEN'
    finding HTML links ... done
    CGEN                                    html  
    GxE.scan                                html  
    GxE.scan.combine                        html  
    GxE.scan.partition                      html  
    LocusMapData                            html  
    QQ.plot                                 html  
    Xdata                                   html  
    additive.test                           html  
    chromosome.plot                         html  
    getMatchedSets                          html  
    getSummary                              html  
    getWaldTest                             html  
    locusMap.list                           html  
    pheno.list                              html  
    printEffects                            html  
    snp.effects                             html  
    snp.effects.plot                        html  
    snp.list                                html  
    snp.logistic                            html  
    snp.matched                             html  
    snp.score                               html  
    subject.list                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CGEN' ...
** 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 Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
                   ^
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
                         ^
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 CML.c -o CML.o
CML.c:132:13: warning: 'print_dVec' defined but not used [-Wunused-function]
 static void print_dVec(vec, n, name)
             ^
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 ccl.c -o ccl.o
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c csclust.f -o csclust.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 fsclust.c -o fsclust.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 hcl.c -o hcl.o
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^
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 pmatch.c -o pmatch.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 score.c -o score.o
score.c: In function 'infoSmallStandard':
score.c:18:27: warning: unused variable 'ii' [-Wunused-variable]
   int  nr, nc, i, j, row, ii, nc2;
                           ^
score.c: In function 'getScoreEB':
score.c:183:21: warning: unused variable 'p6' [-Wunused-variable]
   double *p4, *p5, *p6;
                     ^
score.c:183:16: warning: unused variable 'p5' [-Wunused-variable]
   double *p4, *p5, *p6;
                ^
score.c:183:11: warning: unused variable 'p4' [-Wunused-variable]
   double *p4, *p5, *p6;
           ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.16.0.zip
* DONE (CGEN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CGEN' successfully unpacked and MD5 sums checked
In R CMD INSTALL