Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:11:15 -0400 (Wed, 15 Apr 2020).
Package 1545/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
scran 1.14.6 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: scran |
Version: 1.14.6 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scran |
StartedAt: 2020-04-14 18:50:07 -0400 (Tue, 14 Apr 2020) |
EndedAt: 2020-04-14 18:53:21 -0400 (Tue, 14 Apr 2020) |
EllapsedTime: 194.2 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘scran’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c build_snn.cpp -o build_snn.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c calc_log_count_stats.cpp -o calc_log_count_stats.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c combine_rho.cpp -o combine_rho.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c combine_simes.cpp -o combine_simes.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_CV2.cpp -o compute_CV2.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_blocked_stats.cpp -o compute_blocked_stats.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_rho_null.cpp -o compute_rho_null.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_rho_pairs.cpp -o compute_rho_pairs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c cyclone_scores.cpp -o cyclone_scores.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c fit_linear_model.cpp -o fit_linear_model.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_residuals.cpp -o get_residuals.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_scaled_ranks.cpp -o get_scaled_ranks.o get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’: get_scaled_ranks.cpp:137:100: required from here get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable] double accumulated_rank=0; ^~~~~~~~~~~~~~~~ get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’: get_scaled_ranks.cpp:139:100: required from here get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable] g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c overlap_exprs.cpp -o overlap_exprs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c pool_size_factors.cpp -o pool_size_factors.o pool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’: pool_size_factors.cpp:36:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); } ~~~~~~^~~~~~~~~~~~~~~~~~~~ pool_size_factors.cpp:39:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (order.size() < ncells*2-1) { throw std::runtime_error("ordering vector is too short for number of cells"); } ~~~~~~~~~~~~~^~~~~~~~~~~~ pool_size_factors.cpp:101:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (auto i=0; i<n; ++i, ++val, ++idx) { ~^~ In file included from pool_size_factors.cpp:4:0: /home/biocbuild/bbs-3.10-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]’: pool_size_factors.cpp:52:34: required from here /home/biocbuild/bbs-3.10-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()) { g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c rand_custom.cpp -o rand_custom.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c run_dormqr.cpp -o run_dormqr.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c shuffle_matrix.cpp -o shuffle_matrix.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c subset_and_divide.cpp -o subset_and_divide.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o scran.so RcppExports.o build_snn.o calc_log_count_stats.o combine_rho.o combine_simes.o compute_CV2.o compute_blocked_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o fit_linear_model.o get_residuals.o get_scaled_ranks.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-scran/00new/scran/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 (scran)