Xiuwen Zheng
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SAIGEgds |
| Branch: RELEASE_3_10 |
| Last Commit: 39ef568 |
| Last Changed Date: 2020-04-08 18:49:04 -0400 (Wed, 08 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:33:18 -0400 (Wed, 15 Apr 2020).
| Package 1509/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SAIGEgds 1.0.2 Xiuwen Zheng
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SAIGEgds |
| Version: 1.0.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SAIGEgds_1.0.2.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.0.2.zip && rm SAIGEgds_1.0.2.tar.gz SAIGEgds_1.0.2.zip |
| StartedAt: 2020-04-14 19:37:08 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:38:27 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 79.0 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SAIGEgds_1.0.2.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.0.2.zip && rm SAIGEgds_1.0.2.tar.gz SAIGEgds_1.0.2.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 1395k 100 1395k 0 0 3477k 0 --:--:-- --:--:-- --:--:-- 3514k
install for i386
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c SPATest.cpp -o SPATest.o
SPATest.cpp: In function 'double Saddle_Prob_Fast(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)':
SPATest.cpp:217:40: warning: 'NAsigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
double k2 = K2(t, n_nonzero, mu, g) + NAsigma;
^
SPATest.cpp:308:15: note: 'NAsigma' was declared here
double NAmu, NAsigma;
^
SPATest.cpp:216:47: warning: 'NAmu' may be used uninitialized in this function [-Wmaybe-uninitialized]
double K = Korg(t, n_nonzero, mu, g) + NAmu * t + 0.5 * NAsigma * t * t;
^
SPATest.cpp:308:9: note: 'NAmu' was declared here
double NAmu, NAsigma;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c saige_fitnull.cpp -o saige_fitnull.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c saige_main.cpp -o saige_main.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c vectorization.cpp -o vectorization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SAIGEgds'
finding HTML links ... done
SAIGEgds-package html
seqAssocGLMM_SPA html
finding level-2 HTML links ... done
seqFitNullGLMM_SPA html
seqSAIGE_LoadPval 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 'SAIGEgds' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c SPATest.cpp -o SPATest.o
SPATest.cpp: In function 'double Saddle_Prob_Fast(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)':
SPATest.cpp:217:40: warning: 'NAsigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
double k2 = K2(t, n_nonzero, mu, g) + NAsigma;
^
SPATest.cpp:308:15: note: 'NAsigma' was declared here
double NAmu, NAsigma;
^
SPATest.cpp:166:53: warning: 'NAmu' may be used uninitialized in this function [-Wmaybe-uninitialized]
double newK1 = K1_adj(tnew, n_nonzero, mu, g, q) +
^
SPATest.cpp:308:9: note: 'NAmu' was declared here
double NAmu, NAsigma;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c saige_fitnull.cpp -o saige_fitnull.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c saige_main.cpp -o saige_main.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mtune=core2 -c vectorization.cpp -o vectorization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.0.2.zip
* DONE (SAIGEgds)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SAIGEgds' successfully unpacked and MD5 sums checked