Multiple platform build/check report for BioC 3.9 - INSTALL report for batchelor on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL batchelor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘batchelor’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function ‘SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
adjust_shift_variance.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t other=0; other<restricted1.size(); ++other) {
                                  ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cosine_norm.cpp -o cosine_norm.o
In file included from cosine_norm.cpp:6:0:
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
cosine_norm.cpp:50:22:   required from ‘SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’
cosine_norm.cpp:70:79:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
cosine_norm.cpp:50:22:   required from ‘SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’
cosine_norm.cpp:72:79:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c find_mutual_nns.cpp -o find_mutual_nns.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function ‘SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)’:
smooth_gaussian_kernel.cpp:20:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) {
         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c unlog_exprs.cpp -o unlog_exprs.o
unlog_exprs.cpp: In function ‘SEXPREC* unlog_exprs_scaled(SEXP, SEXP, SEXP, SEXP, SEXP)’:
unlog_exprs.cpp:51:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (slen!=rescaling.size()) {
         ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘Rcpp::IntegerVector check_subset_vector(SEXP, size_t)’:
utils.cpp:9:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (isNA(s) || s < 0 || s >= len) {
                                 ˜˜^˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o batchelor.so adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-batchelor/00new/batchelor/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (batchelor)
INSTALL report for batchelor on malbec2

Summary

Command output
