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CHECK report for scran on malbec1

This page was generated on 2019-04-16 11:52:01 -0400 (Tue, 16 Apr 2019).

Package 1405/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.10.2
Aaron Lun
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/scran
Branch: RELEASE_3_8
Last Commit: b4191ec
Last Changed Date: 2019-01-04 13:12:28 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scran
Version: 1.10.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scran_1.10.2.tar.gz
StartedAt: 2019-04-16 02:56:01 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:04:21 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 499.6 seconds
RetCode: 0
Status:  OK 
CheckDir: scran.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scran_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/scran.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.10.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scran’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/scran.Rcheck/00check.log’
for details.

Installation output

scran.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL scran
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘scran’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c combine_simes.cpp -o combine_simes.o
combine_simes.cpp: In function ‘SEXPREC* combine_simes(SEXP, SEXP)’:
combine_simes.cpp:15:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         } else if (ngenes!=current.size()) {
                          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c compute_CV2.cpp -o compute_CV2.o
compute_CV2.cpp: In instantiation of ‘SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’:
compute_CV2.cpp:74:83:   required from here
compute_CV2.cpp:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sizefacs.size()!=ncells) { 
                            ^
compute_CV2.cpp: In instantiation of ‘SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’:
compute_CV2.cpp:77:83:   required from here
compute_CV2.cpp:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from compute_CV2.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
compute_CV2.cpp:80:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
compute_CV2.cpp:80:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In member function ‘std::vector<long unsigned int> cache_manager::reorder(Rcpp::IntegerVector, Rcpp::IntegerVector)’:
compute_rho.cpp:246:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (npairs!=g2.size()) {
                   ^
compute_rho.cpp:259:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g1x < 0 || g1x >= Ngenes) {
                                ^
compute_rho.cpp:262:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g2x < 0 || g2x >= Ngenes) {
                                ^
compute_rho.cpp: In function ‘SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
compute_rho.cpp:338:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Npairs!=second.size()) { 
               ^
compute_rho.cpp:343:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Rho.size()!=Npairs) { 
                   ^
compute_rho.cpp:348:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Pval.size()!=Npairs) {
                    ^
compute_rho.cpp:353:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Limited.size()!=Npairs) { 
                       ^
compute_rho.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Order.size()!=Npairs) { 
                     ^
compute_rho.cpp: In instantiation of ‘SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’:
compute_rho.cpp:175:114:   required from here
compute_rho.cpp:159:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int cs=0; cs<cslen; ++cs, ++iIt){ 
                          ^
compute_rho.cpp: In instantiation of ‘SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’:
compute_rho.cpp:180:117:   required from here
compute_rho.cpp:159:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from compute_rho.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
compute_rho.cpp:406:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
compute_rho.cpp:406:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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:110:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) { 
               ^
find_mutual_nns.cpp:125:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i >= averages.size() || averages[i].size()==0) { 
                   ^
find_mutual_nns.cpp:126:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (i >= averages.size()) { 
                       ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from find_mutual_nns.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
find_mutual_nns.cpp:348:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
find_mutual_nns.cpp:348:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c fit_linear_model.cpp -o fit_linear_model.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from fit_linear_model.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
fit_linear_model.cpp:139:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
fit_linear_model.cpp:139:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c forge_system.cpp -o forge_system.o
forge_system.cpp: In function ‘SEXPREC* forge_system(SEXP, SEXP, SEXP, SEXP)’:
forge_system.cpp:20:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (SIZE < 1 || SIZE > ncells) { throw std::runtime_error("each element of sizes should be within [1, number of cells]"); }
                              ^
forge_system.cpp:28:15: 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"); }
               ^
forge_system.cpp:32:22: 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"); }
                      ^
forge_system.cpp:34:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (o < 0 || o > ncells) { 
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from forge_system.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
forge_system.cpp:127:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c get_residuals.cpp -o get_residuals.o
get_residuals.cpp: In function ‘SEXPREC* get_residuals(SEXP, SEXP, SEXP, SEXP, SEXP)’:
get_residuals.cpp:39:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int c=0; c<ncells; ++c, ++tIt) {
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from get_residuals.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
get_residuals.cpp:64:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c get_scaled_ranks.cpp -o get_scaled_ranks.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from get_scaled_ranks.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
get_scaled_ranks.cpp:113:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
get_scaled_ranks.cpp:113:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c overlap_exprs.cpp -o overlap_exprs.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from overlap_exprs.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
overlap_exprs.cpp:152:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
overlap_exprs.cpp:152:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from shuffle_matrix.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
shuffle_matrix.cpp:33:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
shuffle_matrix.cpp:33:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of ‘SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
shuffle_scores.cpp:118:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
shuffle_scores.cpp: In instantiation of ‘SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
shuffle_scores.cpp:121:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from shuffle_scores.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
shuffle_scores.cpp:156:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
shuffle_scores.cpp:156:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c simple_sum_factors.cpp -o simple_sum_factors.o
simple_sum_factors.cpp: In instantiation of ‘SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
simple_sum_factors.cpp:122:123:   required from here
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
simple_sum_factors.cpp: In instantiation of ‘SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
simple_sum_factors.cpp:125:124:   required from here
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from simple_sum_factors.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
simple_sum_factors.cpp:128:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
simple_sum_factors.cpp:128:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c subset_and_divide.cpp -o subset_and_divide.o
subset_and_divide.cpp: In instantiation of ‘SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’:
subset_and_divide.cpp:93:108:   required from here
subset_and_divide.cpp:28:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (scale_values.size()!=in->get_ncol()) {
                                ^
subset_and_divide.cpp: In instantiation of ‘SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’:
subset_and_divide.cpp:96:108:   required from here
subset_and_divide.cpp:28:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scran.h:4,
                 from subset_and_divide.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
subset_and_divide.cpp:99:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
subset_and_divide.cpp:99:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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:6:35: 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-3.8-bioc/R/lib -L/usr/local/lib -o scran.so build_snn.o calc_log_count_stats.o combine_simes.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_matrix.o shuffle_scores.o simple_sum_factors.o subset_and_divide.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (scran)

Tests output

scran.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(testthat)
> library(scran)
Loading required package: BiocParallel
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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
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


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

> test_check("scran")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8611 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
282.012   2.884 285.251

Example timings

scran.Rcheck/scran-Ex.timings

nameusersystemelapsed
DM0.1040.0000.104
buildSNNGraph0.080.000.08
cleanSizeFactors0.5040.0000.504
clusterModularity0.2800.0040.294
combineMarkers1.2320.0161.251
combinePValues0.0160.0040.017
combineVar1.4920.0281.523
computeSpikeFactors0.1920.0000.191
computeSumFactors2.3160.0242.341
convertTo4.0560.0844.144
correlatePairs0.260.000.26
cosineNorm0.0000.0040.007
cyclone0.3400.0040.364
decomposeVar2.0080.0202.030
denoisePCA0.0440.0040.048
doubletCells1.0280.0081.037
doubletCluster0.3760.0040.382
fastMNN0.4280.0000.430
findMarkers0.3520.0000.355
improvedCV20.3320.0040.337
makeTechTrend0.0320.0000.031
mnnCorrect0.0320.0000.032
multiBatchNorm0.2840.0000.282
multiBatchPCA0.1360.0000.135
multiBlockNorm0.9960.0041.001
multiBlockVar1.4480.0081.456
overlapExprs0.4600.0000.461
pairwiseTTests0.3360.0000.336
pairwiseWilcox0.3760.0080.383
parallelPCA0.3520.0080.360
quickCluster0.8280.0040.830
sandbag0.2240.0040.226
scaledColRanks0.1120.0000.110
simpleSumFactors1.8200.0041.824
technicalCV20.3120.0040.318
testVar0.0400.0000.037
trendVar0.8320.0120.844