scater 1.11.15
Davis McCarthy
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: master |
| Last Commit: 30a42c8 |
| Last Changed Date: 2019-04-07 14:45:06 -0400 (Sun, 07 Apr 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scater
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scater’ ...
** 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 calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19: required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:144:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19: required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:146:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
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 combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function ‘void check_topset(const IntegerVector&)’:
combined_qc.cpp:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t t=1; t<top.size(); ++t) {
˜^˜˜˜˜˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61: required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:285:74: required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
˜^˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61: required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:287:74: required from here
combined_qc.cpp:35:35: 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 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 num_exprs.cpp -o num_exprs.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 sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function ‘SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)’:
sum_counts.cpp:72:18: warning: unused variable ‘ncells’ [-Wunused-variable]
const size_t ncells=end_index - start_index;
^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:150:83: required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
const size_t ncells=mat->get_ncol();
^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:154:83: required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
/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]’:
sum_counts.cpp:120:22: required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:150:83: 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]’:
sum_counts.cpp:120:22: required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:154:83: 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 utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-scater/00new/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘scater’
** 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 (scater)