scde 2.16.0
Jean Fan
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/scde |
| Branch: RELEASE_3_11 |
| Last Commit: 725565d |
| Last Changed Date: 2020-04-27 14:52:39 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.16.0.tar.gz
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install for i386
* installing *source* package 'scde' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
~^~~~~~~~~~~~~~
bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i=0;i<target.n_cols;i++) {
~^~~~~~~~~~~~~~
bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
~^~~~~~~~~~~~~~
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
~^~~~~~~~~~~~~~~
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i=0;i<target1.n_cols;i++) {
~^~~~~~~~~~~~~~~
bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
double maxv=nbp.max(maxij);
^~~~
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
double maxv=nbp.max(maxij);
^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/scde.buildbin-libdir/00LOCK-scde/00new/scde/libs/i386
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scde'
finding HTML links ... done
ViewPagodaApp-class html
bwpca html
clean.counts html
clean.gos html
es.mef.small html
knn html
knn.error.models html
make.pagoda.app html
o.ifm html
pagoda.cluster.cells html
pagoda.effective.cells html
pagoda.gene.clusters html
pagoda.pathway.wPCA html
pagoda.reduce.loading.redundancy html
pagoda.reduce.redundancy html
pagoda.show.pathways html
pagoda.subtract.aspect html
pagoda.top.aspects html
pagoda.varnorm html
pagoda.view.aspects html
papply html
pollen html
scde html
scde.browse.diffexp html
scde.edff html
scde.error.models html
scde.expression.difference html
scde.expression.magnitude html
scde.expression.prior html
scde.failure.probability html
scde.fit.models.to.reference html
scde.posteriors html
scde.test.gene.expression.difference html
show.app html
view.aspects html
winsorize.matrix 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 'scde' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
~^~~~~~~~~~~~~~
bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i=0;i<target.n_cols;i++) {
~^~~~~~~~~~~~~~
bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
~^~~~~~~~~~~~~~
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
~^~~~~~~~~~~~~~~
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i=0;i<target1.n_cols;i++) {
~^~~~~~~~~~~~~~~
bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
double maxv=nbp.max(maxij);
^~~~
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
double maxv=nbp.max(maxij);
^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/scde.buildbin-libdir/scde/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scde' as scde_2.16.0.zip
* DONE (scde)