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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:52 -0400 (Wed, 17 Oct 2018).
| Package 212/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CGEN 3.16.0 William Wheeler
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### 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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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