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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:37 -0400 (Wed, 16 Oct 2019).
| Package 1477/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scran 1.12.1 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scran |
| Version: 1.12.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scran.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scran_1.12.1.tar.gz |
| StartedAt: 2019-10-16 06:58:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:13:22 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 911.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scran.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scran.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scran_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scran.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scran/DESCRIPTION' ... OK * this is package 'scran' version '1.12.1' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scran' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/scran/libs/i386/scran.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/scran/libs/x64/scran.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scran.Rcheck/00check.log' for details.
scran.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scran_1.12.1.tar.gz && rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scran.buildbin-libdir scran_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scran_1.12.1.zip && rm scran_1.12.1.tar.gz scran_1.12.1.zip
###
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install for i386
* installing *source* package 'scran' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c calc_log_count_stats.cpp -o calc_log_count_stats.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_rho.cpp -o combine_rho.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_rho_null.cpp -o compute_rho_null.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from compute_rho_null.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_rho_pairs.cpp -o compute_rho_pairs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cyclone_scores.cpp -o cyclone_scores.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from cyclone_scores.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_residuals.cpp -o get_residuals.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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
C:/Users/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()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rand_custom.cpp -o rand_custom.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from rand_custom.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from shuffle_matrix.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c subset_and_divide.cpp -o subset_and_divide.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test_shuffle.cpp -o test_shuffle.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from test_shuffle.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def 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 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scran.buildbin-libdir/00LOCK-scran/00new/scran/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scran'
finding HTML links ... done
DM html
buildSNNGraph html
finding level-2 HTML links ... done
cleanSizeFactors html
clusterModularity html
combineMarkers html
combinePValues html
combineVar html
computeSpikeFactors html
computeSumFactors html
convertTo html
correlateGenes html
correlatePairs html
cosineNorm html
cyclone html
decomposeVar html
denoisePCA html
doubletCells html
doubletCluster html
fastMNN html
findMarkers html
gene_selection html
improvedCV2 html
makeTechTrend html
mnnCorrect html
multiBatchNorm html
multiBatchPCA html
multiBlockNorm html
multiBlockVar html
overlapExprs html
pairwiseTTests html
pairwiseWilcox html
parallelPCA html
quickCluster html
sandbag html
scaledColRanks html
technicalCV2 html
testVar html
trendVar 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 'scran' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c calc_log_count_stats.cpp -o calc_log_count_stats.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_rho.cpp -o combine_rho.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_rho_null.cpp -o compute_rho_null.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from compute_rho_null.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_rho_pairs.cpp -o compute_rho_pairs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cyclone_scores.cpp -o cyclone_scores.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from cyclone_scores.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_residuals.cpp -o get_residuals.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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
C:/Users/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()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rand_custom.cpp -o rand_custom.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from rand_custom.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from shuffle_matrix.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c subset_and_divide.cpp -o subset_and_divide.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test_shuffle.cpp -o test_shuffle.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
from rand_custom.h:6,
from test_shuffle.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def 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 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.12.1.zip
* DONE (scran)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked
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scran.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(scran)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> test_check("scran")
== testthat results ===========================================================
[ OK: 11683 | SKIPPED: 2 | WARNINGS: 318 | FAILED: 0 ]
>
> proc.time()
user system elapsed
302.21 9.29 311.96
|
scran.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(scran)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> test_check("scran")
== testthat results ===========================================================
[ OK: 11683 | SKIPPED: 2 | WARNINGS: 308 | FAILED: 0 ]
>
> proc.time()
user system elapsed
230.28 4.28 235.79
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scran.Rcheck/examples_i386/scran-Ex.timings
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scran.Rcheck/examples_x64/scran-Ex.timings
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