Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for CGEN on tokay1

This page was generated on 2020-08-10 12:12:52 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CGEN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 255/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.25.1
William Wheeler
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/CGEN
Branch: master
Last Commit: adf5934
Last Changed Date: 2020-06-01 09:59:32 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: CGEN
Version: 3.25.1
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CGEN_3.25.1.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.25.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CGEN_3.25.1.zip && rm CGEN_3.25.1.tar.gz CGEN_3.25.1.zip
StartedAt: 2020-08-09 16:51:26 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 16:52:18 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CGEN_3.25.1.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.25.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CGEN_3.25.1.zip && rm CGEN_3.25.1.tar.gz CGEN_3.25.1.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  641k  100  641k    0     0  17.1M      0 --:--:-- --:--:-- --:--:-- 18.9M

install for i386

* installing *source* package 'CGEN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign -c csclust.f -o csclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fsclust.c -o fsclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatch.c -o pmatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/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 from temporary location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CGEN' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign -c csclust.f -o csclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fsclust.c -o fsclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatch.c -o pmatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64
** testing if installed package can be loaded
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.25.1.zip
* DONE (CGEN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CGEN' successfully unpacked and MD5 sums checked