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CHECK report for cydar on tokay2

This page was generated on 2019-04-09 12:30:31 -0400 (Tue, 09 Apr 2019).

Package 373/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cydar 1.7.3
Aaron Lun
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cydar
Branch: master
Last Commit: ade00bf
Last Changed Date: 2019-02-28 11:37:32 -0400 (Thu, 28 Feb 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: cydar
Version: 1.7.3
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cydar.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cydar_1.7.3.tar.gz
StartedAt: 2019-04-09 02:07:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:14:43 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 441.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cydar.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cydar.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cydar_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cydar.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cydar/DESCRIPTION' ... OK
* this is package 'cydar' version '1.7.3'
* 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 'cydar' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/normalizeBatch.Rd:125: file link 'normalization' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/outlierGate.Rd:38: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:26: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:36: file link 'flowFrame' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:38: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cydar.Rcheck/00install.out' for details.
* 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 ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
  See the note in ?`:::` about the use of this operator.
* 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 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/cydar/libs/i386/cydar.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/cydar/libs/x64/cydar.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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/cydar.Rcheck/00check.log'
for details.

Installation output

cydar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cydar_1.7.3.tar.gz && rm -rf cydar.buildbin-libdir && mkdir cydar.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cydar.buildbin-libdir cydar_1.7.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cydar_1.7.3.zip && rm cydar_1.7.3.tar.gz cydar_1.7.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 57591  100 57591    0     0  1167k      0 --:--:-- --:--:-- --:--:-- 1307k

install for i386

* installing *source* package 'cydar' ...
** 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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_density.cpp -o compute_density.o
compute_density.cpp: In function 'SEXPREC* compute_density(SEXP, SEXP)':
compute_density.cpp:10:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<Distances.size(); ++i) {
                       ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Samples.size()!=ncells) { 
                       ^
compute_hyperstats.cpp:60:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t icx=0; icx<curass.size(); ++icx) {
                                   ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Samples.size()!=ncells) { 
                       ^
compute_median_int.cpp:41:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex <= 0 || curdex > ncells) {
                                       ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c drop_redundant.cpp -o drop_redundant.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:/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:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o drop_redundant.o init.o utils.o -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/cydar.buildbin-libdir/00LOCK-cydar/00new/cydar/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cydar'
    finding HTML links ... done
    CyData                                  html  
    finding level-2 HTML links ... done

    countCells                              html  
    createColorBar                          html  
    dnaGate                                 html  
    expandRadius                            html  
    findFirstSphere                         html  
    intensityRanges                         html  
    interpretSpheres                        html  
    labelSpheres                            html  
    medIntensities                          html  
    multiIntHist                            html  
    neighborDistances                       html  
    normalizeBatch                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/normalizeBatch.Rd:125: file link 'normalization' in package 'flowCore' does not exist and so has been treated as a topic
    outlierGate                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/outlierGate.Rd:38: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
    pickBestMarkers                         html  
    plotSphereIntensity                     html  
    plotSphereLogFC                         html  
    poolCells                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:26: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:36: file link 'flowFrame' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAT6VbG/R.INSTALL18074bf4962/cydar/man/poolCells.Rd:38: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    prepareCellData                         html  
    spatialFDR                              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 'cydar' ...
** 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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_density.cpp -o compute_density.o
compute_density.cpp: In function 'SEXPREC* compute_density(SEXP, SEXP)':
compute_density.cpp:10:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<Distances.size(); ++i) {
                       ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Samples.size()!=ncells) { 
                       ^
compute_hyperstats.cpp:60:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t icx=0; icx<curass.size(); ++icx) {
                                   ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Samples.size()!=ncells) { 
                       ^
compute_median_int.cpp:41:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex <= 0 || curdex > ncells) {
                                       ^
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:/extsoft/include"     -O2 -Wall  -mtune=generic -c drop_redundant.cpp -o drop_redundant.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:/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:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o drop_redundant.o init.o utils.o -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/cydar.buildbin-libdir/cydar/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cydar' as cydar_1.7.3.zip
* DONE (cydar)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cydar' successfully unpacked and MD5 sums checked

Tests output

cydar.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(cydar)
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, 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

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


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("cydar")

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...

Estimating landmarks for channel X3 ...
Registering curves for parameter X3 ...

Estimating landmarks for channel X4 ...
Registering curves for parameter X4 ...

Estimating landmarks for channel X5 ...
Registering curves for parameter X5 ...

Estimating landmarks for channel X6 ...
Registering curves for parameter X6 ...

Estimating landmarks for channel X7 ...
Registering curves for parameter X7 ...

Estimating landmarks for channel X8 ...
Registering curves for parameter X8 ...

Estimating landmarks for channel X9 ...
Registering curves for parameter X9 ...

Estimating landmarks for channel X10 ...
Registering curves for parameter X10 ...

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...

Estimating landmarks for channel X3 ...
Registering curves for parameter X3 ...

Estimating landmarks for channel X4 ...
Registering curves for parameter X4 ...

Estimating landmarks for channel X5 ...
Registering curves for parameter X5 ...

Estimating landmarks for channel X6 ...
Registering curves for parameter X6 ...

Estimating landmarks for channel X7 ...
Registering curves for parameter X7 ...

Estimating landmarks for channel X8 ...
Registering curves for parameter X8 ...

Estimating landmarks for channel X9 ...
Registering curves for parameter X9 ...

Estimating landmarks for channel X10 ...
Registering curves for parameter X10 ...
== testthat results  ===========================================================
OK: 292 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  53.51    1.98   82.03

cydar.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(cydar)
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, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
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    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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> test_check("cydar")

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...

Estimating landmarks for channel X3 ...
Registering curves for parameter X3 ...

Estimating landmarks for channel X4 ...
Registering curves for parameter X4 ...

Estimating landmarks for channel X5 ...
Registering curves for parameter X5 ...

Estimating landmarks for channel X6 ...
Registering curves for parameter X6 ...

Estimating landmarks for channel X7 ...
Registering curves for parameter X7 ...

Estimating landmarks for channel X8 ...
Registering curves for parameter X8 ...

Estimating landmarks for channel X9 ...
Registering curves for parameter X9 ...

Estimating landmarks for channel X10 ...
Registering curves for parameter X10 ...

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...

Estimating landmarks for channel X3 ...
Registering curves for parameter X3 ...

Estimating landmarks for channel X4 ...
Registering curves for parameter X4 ...

Estimating landmarks for channel X5 ...
Registering curves for parameter X5 ...

Estimating landmarks for channel X6 ...
Registering curves for parameter X6 ...

Estimating landmarks for channel X7 ...
Registering curves for parameter X7 ...

Estimating landmarks for channel X8 ...
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Estimating landmarks for channel X9 ...
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Estimating landmarks for channel X10 ...
Registering curves for parameter X10 ...
== testthat results  ===========================================================
OK: 292 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  37.64    1.12   72.96

Example timings

cydar.Rcheck/examples_i386/cydar-Ex.timings

nameusersystemelapsed
CyData1.210.051.25
countCells1.350.001.35
createColorBar000
dnaGate0.380.100.50
expandRadius0.420.000.42
findFirstSphere0.100.000.09
intensityRanges0.610.000.61
interpretSpheres0.870.000.88
labelSpheres0.020.000.01
medIntensities0.50.00.5
multiIntHist000
neighborDistances0.610.000.61
normalizeBatch0.220.000.22
outlierGate0.780.000.88
pickBestMarkers0.50.00.5
plotSphereIntensity0.020.000.02
plotSphereLogFC0.010.000.01
poolCells0.990.061.05
prepareCellData0.550.000.55
spatialFDR0.070.000.08

cydar.Rcheck/examples_x64/cydar-Ex.timings

nameusersystemelapsed
CyData1.670.001.67
countCells0.600.000.61
createColorBar0.010.000.01
dnaGate0.350.030.38
expandRadius0.610.000.61
findFirstSphere0.070.000.08
intensityRanges1.190.001.19
interpretSpheres0.690.020.70
labelSpheres0.020.000.02
medIntensities0.400.010.42
multiIntHist0.020.000.02
neighborDistances1.150.031.18
normalizeBatch0.180.020.19
outlierGate0.480.000.48
pickBestMarkers0.30.00.3
plotSphereIntensity0.010.020.03
plotSphereLogFC000
poolCells1.020.001.02
prepareCellData0.450.000.45
spatialFDR0.060.000.06