Aaron Lun
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/scran |
| Branch: RELEASE_3_10 |
| Last Commit: 240fad2 |
| Last Changed Date: 2020-01-30 00:15:28 -0400 (Thu, 30 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:16 -0400 (Wed, 15 Apr 2020).
| Package 1545/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scran 1.14.6 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: scran |
| Version: 1.14.6 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scran_1.14.6.tar.gz |
| StartedAt: 2020-04-15 03:45:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:56:24 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 648.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scran.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scran_1.14.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scran.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.6’
* 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 23.6Mb
sub-directories of 1Mb or more:
libs 22.5Mb
* 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 ... WARNING
Found the following significant warnings:
Warning: handling of spike-ins via 'isSpike()' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'decomposeVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'decomposeVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: 'clusters=' is deprecated.
Warning: 'improvedCV2' is deprecated.
Warning: handling of spike-ins via 'isSpike()' is deprecated.
Warning: 'multiBlockNorm' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: handling of spike-ins via 'isSpike()' is deprecated.
Warning: 'multiBlockNorm' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'multiBlockVar' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'decomposeVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'decomposeVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'decomposeVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: handling of spike-ins via 'isSpike()' is deprecated.
Warning: 'overlapExprs' is deprecated.
Warning: 'parallelPCA' is deprecated.
Warning: 'technicalCV2' is deprecated.
Warning: 'isSpike<-' is deprecated.
Warning: 'spikeNames' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'technicalCV2' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: 'testVar' is deprecated.
Warning: handling of spike-ins via 'isSpike()' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: 'trendVar' is deprecated.
Warning: 'trendVar' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
cyclone 11.412 0.020 11.453
bootstrapCluster 10.740 0.048 10.819
doubletCells 6.228 0.172 6.422
computeSumFactors 6.196 0.112 6.314
buildSNNGraph 5.564 0.020 5.593
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/scran.Rcheck/00check.log’
for details.
scran.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scran
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘scran’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c build_snn.cpp -o build_snn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c calc_log_count_stats.cpp -o calc_log_count_stats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c combine_rho.cpp -o combine_rho.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c combine_simes.cpp -o combine_simes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_CV2.cpp -o compute_CV2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_blocked_stats.cpp -o compute_blocked_stats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_rho_null.cpp -o compute_rho_null.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c compute_rho_pairs.cpp -o compute_rho_pairs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c cyclone_scores.cpp -o cyclone_scores.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c fit_linear_model.cpp -o fit_linear_model.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_residuals.cpp -o get_residuals.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_scaled_ranks.cpp -o get_scaled_ranks.o
get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’:
get_scaled_ranks.cpp:137:100: required from here
get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable]
double accumulated_rank=0;
^~~~~~~~~~~~~~~~
get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’:
get_scaled_ranks.cpp:139:100: required from here
get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c overlap_exprs.cpp -o overlap_exprs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c pool_size_factors.cpp -o pool_size_factors.o
pool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’:
pool_size_factors.cpp:36:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
~~~~~~^~~~~~~~~~~~~~~~~~~~
pool_size_factors.cpp:39:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (order.size() < ncells*2-1) { throw std::runtime_error("ordering vector is too short for number of cells"); }
~~~~~~~~~~~~~^~~~~~~~~~~~
pool_size_factors.cpp:101:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i<n; ++i, ++val, ++idx) {
~^~
In file included from pool_size_factors.cpp:4:0:
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
pool_size_factors.cpp:52:34: required from here
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c rand_custom.cpp -o rand_custom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c run_dormqr.cpp -o run_dormqr.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c shuffle_matrix.cpp -o shuffle_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c subset_and_divide.cpp -o subset_and_divide.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o scran.so RcppExports.o build_snn.o calc_log_count_stats.o combine_rho.o combine_simes.o compute_CV2.o compute_blocked_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o fit_linear_model.o get_residuals.o get_scaled_ranks.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-scran/00new/scran/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scran)
scran.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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: 5798 | SKIPPED: 0 | WARNINGS: 845 | FAILED: 0 ]
>
> proc.time()
user system elapsed
338.296 5.672 344.673
scran.Rcheck/scran-Ex.timings
| name | user | system | elapsed | |
| DM | 0.044 | 0.004 | 0.048 | |
| bootstrapCluster | 10.740 | 0.048 | 10.819 | |
| buildSNNGraph | 5.564 | 0.020 | 5.593 | |
| cleanSizeFactors | 0.048 | 0.000 | 0.046 | |
| clusterModularity | 2.276 | 0.004 | 2.280 | |
| combineMarkers | 1.304 | 0.004 | 1.320 | |
| combinePValues | 0.048 | 0.000 | 0.046 | |
| combineVar | 1.252 | 0.016 | 1.269 | |
| computeSpikeFactors | 0.812 | 0.012 | 0.825 | |
| computeSumFactors | 6.196 | 0.112 | 6.314 | |
| convertTo | 2.836 | 0.032 | 2.874 | |
| correlateGenes | 0.920 | 0.000 | 0.917 | |
| correlateNull | 0.272 | 0.004 | 0.274 | |
| correlatePairs | 1.752 | 0.008 | 1.763 | |
| cyclone | 11.412 | 0.020 | 11.453 | |
| decomposeVar | 1.436 | 0.004 | 1.459 | |
| denoisePCA | 1.620 | 0.008 | 1.640 | |
| doubletCells | 6.228 | 0.172 | 6.422 | |
| doubletCluster | 0.416 | 0.000 | 0.419 | |
| findMarkers | 2.096 | 0.000 | 2.101 | |
| fitTrendCV2 | 0.556 | 0.004 | 0.561 | |
| fitTrendPoisson | 1.032 | 0.024 | 1.062 | |
| fitTrendVar | 0.616 | 0.000 | 0.615 | |
| getClusteredPCs | 4.020 | 0.080 | 4.109 | |
| getTopHVGs | 0.532 | 0.000 | 0.532 | |
| getTopMarkers | 0.732 | 0.004 | 0.735 | |
| improvedCV2 | 0.18 | 0.00 | 0.18 | |
| makeTechTrend | 0.028 | 0.004 | 0.032 | |
| modelGeneCV2 | 0.904 | 0.012 | 0.919 | |
| modelGeneCV2WithSpikes | 0.616 | 0.000 | 0.616 | |
| modelGeneVar | 1.212 | 0.004 | 1.215 | |
| modelGeneVarByPoisson | 0.904 | 0.004 | 0.920 | |
| modelGeneVarWithSpikes | 0.800 | 0.004 | 0.805 | |
| multiBlockNorm | 1.108 | 0.000 | 1.110 | |
| multiBlockVar | 1.764 | 0.012 | 1.780 | |
| overlapExprs | 0.676 | 0.000 | 0.675 | |
| pairwiseBinom | 0.492 | 0.004 | 0.497 | |
| pairwiseTTests | 0.668 | 0.008 | 0.676 | |
| pairwiseWilcox | 0.488 | 0.004 | 0.490 | |
| parallelPCA | 2.780 | 0.012 | 2.796 | |
| quickCluster | 2.132 | 0.000 | 2.142 | |
| quickSubCluster | 4.564 | 0.008 | 4.592 | |
| sandbag | 0.776 | 0.012 | 1.785 | |
| scaledColRanks | 1.492 | 0.008 | 1.500 | |
| technicalCV2 | 0.536 | 0.004 | 0.541 | |
| testVar | 0.056 | 0.000 | 0.056 | |
| trendVar | 1.468 | 0.000 | 1.470 | |