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CHECK report for scater on malbec2

This page was generated on 2019-04-09 11:44:47 -0400 (Tue, 09 Apr 2019).

Package 1433/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.11.15
Davis McCarthy
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/scater
Branch: master
Last Commit: 30a42c8
Last Changed Date: 2019-04-07 14:45:06 -0400 (Sun, 07 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: scater
Version: 1.11.15
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scater_1.11.15.tar.gz
StartedAt: 2019-04-09 03:28:37 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:36:04 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 447.0 seconds
RetCode: 0
Status:  OK 
CheckDir: scater.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scater_1.11.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scater.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.11.15’
* 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 ‘scater’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_reddim 5.916   0.02   5.947
* 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-3.9-bioc/meat/scater.Rcheck/00check.log’
for details.



Installation output

scater.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scater’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19:   required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:144:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                          ˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) {
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) {
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19:   required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:146:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                          ˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) {
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) {
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function ‘void check_topset(const IntegerVector&)’:
combined_qc.cpp:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<top.size(); ++t) {
                      ˜^˜˜˜˜˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61:   required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:285:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
                                  ˜^˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61:   required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:287:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c num_exprs.cpp -o num_exprs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function ‘SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)’:
sum_counts.cpp:72:18: warning: unused variable ‘ncells’ [-Wunused-variable]
     const size_t ncells=end_index - start_index;
                  ^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:150:83:   required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
     const size_t ncells=mat->get_ncol();
                  ^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:154:83:   required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
/home/biocbuild/bbs-3.9-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<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
sum_counts.cpp:120:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:150:83:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
/home/biocbuild/bbs-3.9-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]’:
sum_counts.cpp:120:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:154:83:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-scater/00new/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘scater’
** 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 (scater)

Tests output

scater.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
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, 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

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

Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

The following object is masked from 'package:stats':

    filter

> 
> test_check("scater")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1227 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
165.126   3.884 219.263 

Example timings

scater.Rcheck/scater-Ex.timings

nameusersystemelapsed
accessors0.7300.0520.782
arrange0.0620.0040.066
bootstraps0.0460.0000.045
calculateAverage0.0600.0000.061
calculateCPM0.0530.0040.058
calculateFPKM0.0460.0040.050
calculateQCMetrics0.280.000.28
calculateTPM0.0840.0000.084
centreSizeFactors0.0570.0000.056
filter0.0660.0000.065
getBMFeatureAnnos000
getExplanatoryPCs0.2720.0940.361
getVarianceExplained0.1430.0160.158
isOutlier0.3000.0120.313
librarySizeFactors0.0120.0000.011
multiplot2.1330.0362.170
mutate0.0370.0040.041
nexprs0.0470.0000.047
normalize0.1150.0080.123
normalizeCounts0.0080.0000.007
plotColData1.9070.0041.987
plotExplanatoryPCs0.7080.0040.712
plotExplanatoryVariables0.6210.0080.629
plotExpression4.640.064.70
plotExprsFreqVsMean1.4110.0161.427
plotExprsVsTxLength2.2520.0122.264
plotHeatmap0.9820.0001.002
plotHighestExprs1.340.001.34
plotPlatePosition0.9460.0000.947
plotRLE2.2340.0202.254
plotReducedDim4.0430.0084.051
plotRowData1.4350.0041.439
plotScater3.4280.0123.440
plot_reddim5.9160.0205.947
readSparseCounts0.0250.0000.025
rename0.0730.0040.076
runDiffusionMap0.2350.0000.236
runMDS0.1230.0040.127
runPCA0.1620.0000.161
runTSNE0.2330.0040.238
runUMAP3.0200.0033.096
sumCountsAcrossCells0.0610.0120.073
sumCountsAcrossFeatures0.0550.0040.058
toSingleCellExperiment000
uniquifyFeatureNames0.0000.0000.001