Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

INSTALL report for scran on malbec2

This page was generated on 2019-10-16 12:08:45 -0400 (Wed, 16 Oct 2019).

Package 1477/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.12.1
Aaron Lun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scran
Branch: RELEASE_3_9
Last Commit: 83c15bd
Last Changed Date: 2019-05-27 01:17:36 -0400 (Mon, 27 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scran
Version: 1.12.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scran
StartedAt: 2019-10-15 19:03:00 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 19:06:38 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 218.4 seconds
RetCode: 0
Status:  OK 

Command output

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


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scran’ ...
** 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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c compute_rho_null.cpp -o compute_rho_null.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from rand_custom.h:6,
                 from compute_rho_null.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cyclone_scores.cpp -o cyclone_scores.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from rand_custom.h:6,
                 from cyclone_scores.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c find_mutual_nns.cpp -o find_mutual_nns.o
find_mutual_nns.cpp: In function ‘SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)’:
find_mutual_nns.cpp:121:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) {
         ~~~~~~^~~~~~~~~~~~~~~
find_mutual_nns.cpp:136:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i >= averages.size() || averages[i].size()==0) {
                 ~~^~~~~~~~~~~~~~~~~~
find_mutual_nns.cpp:137:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (i >= averages.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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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 >; 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 >; 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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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 ‘SEXPREC* pool_size_factors(SEXP, SEXP, SEXP, SEXP)’:
pool_size_factors.cpp:38:15: 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:42:22: 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:104:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (auto i=0; i::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
pool_size_factors.cpp:55:34:   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()) {
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c rand_custom.cpp -o rand_custom.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from rand_custom.h:6,
                 from rand_custom.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from rand_custom.h:6,
                 from shuffle_matrix.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c test_shuffle.cpp -o test_shuffle.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from rand_custom.h:6,
                 from test_shuffle.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
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"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o scran.so build_snn.o calc_log_count_stats.o combine_rho.o combine_simes.o compute_CV2.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o find_mutual_nns.o fit_linear_model.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o test_shuffle.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)