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CHECK report for cydar on merida1

This page was generated on 2019-04-16 12:00:30 -0400 (Tue, 16 Apr 2019).

Package 360/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cydar 1.6.1
Aaron Lun
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/cydar
Branch: RELEASE_3_8
Last Commit: cce42fb
Last Changed Date: 2019-01-04 13:09:15 -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 [ ERROR ] OK 

Summary

Package: cydar
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cydar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cydar_1.6.1.tar.gz
StartedAt: 2019-04-15 23:20:02 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:24:53 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 290.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: cydar.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cydar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cydar_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cydar.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cydar/DESCRIPTION’ ... OK
* this is package ‘cydar’ version ‘1.6.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cydar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  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: 280 SKIPPED: 0 FAILED: 1
  1. Failure: CyData column methods trigger warnings (@test-class.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/cydar.Rcheck/00check.log’
for details.


Installation output

cydar.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cydar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cydar’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_density.cpp -o compute_density.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_hyperstats.cpp -o compute_hyperstats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_median_int.cpp -o compute_median_int.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c drop_redundant.cpp -o drop_redundant.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cydar.so compute_density.o compute_hyperstats.o compute_median_int.o drop_redundant.o init.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/cydar/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 (cydar)

Tests output

cydar.Rcheck/tests/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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("cydar")
── 1. Failure: CyData column methods trigger warnings (@test-class.R#85)  ──────
assay(out) not identical to assay(cn)[, 1:2].
names for current but not for target
Attributes: < names for target but not for current >
Attributes: < Length mismatch: comparison on first 0 components >


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: 280 SKIPPED: 0 FAILED: 1
1. Failure: CyData column methods trigger warnings (@test-class.R#85) 

Error: testthat unit tests failed
Execution halted

Example timings

cydar.Rcheck/cydar-Ex.timings

nameusersystemelapsed
CyData1.2430.0371.297
countCells0.8350.0160.861
createColorBar0.0080.0010.008
dnaGate0.3450.0430.391
expandRadius0.5010.0180.521
findFirstSphere0.5700.0130.593
intensityRanges0.5660.0140.589
interpretSpheres0.9800.0371.025
labelSpheres0.0130.0000.014
medIntensities0.6810.0070.694
multiIntHist0.0080.0010.008
neighborDistances0.7240.0160.742
normalizeBatch0.2440.0250.270
outlierGate0.5790.0220.605
pickBestMarkers0.3920.0070.401
plotSphereIntensity0.0960.0020.099
plotSphereLogFC0.0090.0020.010
poolCells0.9460.0190.968
prepareCellData0.5170.0100.539
spatialFDR0.0750.0010.077