| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:11 -0400 (Thu, 06 May 2021).
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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 267/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CGEN 3.26.1 (landing page) William Wheeler
| malbec1 | Linux (Ubuntu 18.04.5 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 | |||||||||
| Package: CGEN |
| Version: 3.26.1 |
| Command: 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_3.26.1.tar.gz |
| StartedAt: 2021-05-06 08:40:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 08:42:49 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 164.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CGEN_3.26.1.zip |
| PackageFileSize: 1.794 MiB |
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### Running command:
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### 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_3.26.1.tar.gz
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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
** testing if installed package can be loaded from final location
** 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
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.26.1.zip
* DONE (CGEN)