Package: netSmooth

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netSmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netSmooth_1.3.0.tar.gz

StartedAt: 2019-04-09 02:31:45 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:38:29 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 404.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: netSmooth.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netSmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netSmooth_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/netSmooth.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netSmooth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netSmooth’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netSmooth’ 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
robustClusters 4.89  0.249   5.201
* 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:
             ...)
     })
  9: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
  10: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
  11: bploop(structure(list(), class = "lapply"), X, lapply, ARGFUN, BPPARAM)
  12: bploop.lapply(structure(list(), class = "lapply"), X, lapply, ARGFUN, BPPARAM)
  
  thread_monitor No such process in pthread_detach
  thread_monitor No such process in pthread_detach
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 1
  1. Error: netSmooth accepts SingleCellExperiment (@test_netsmooth.R#11) 
  
  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-3.9-bioc/meat/netSmooth.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL netSmooth
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘netSmooth’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (netSmooth)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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(netSmooth)
Loading required package: 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

Loading required package: clusterExperiment

Attaching package: 'clusterExperiment'

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

    plotHeatmap

> 
> test_check("netSmooth")
thread_monitor No such process in pthread_detach
thread_monitor No such process in pthread_detach
── 1. Error: netSmooth accepts SingleCellExperiment (@test_netsmooth.R#11)  ────
attempt to select less than one element in OneIndex
1: netSmooth(smallscRNAseq, smallPPI, alpha = "auto") at testthat/test_netsmooth.R:11
2: netSmooth(smallscRNAseq, smallPPI, alpha = "auto")
3: netSmooth(matrixdata, ...)
4: netSmooth(matrixdata, ...)
5: .local(x, ...)
6: unlist(BiocParallel::bplapply(seq_len(length(smoothed.expression.matrices)), function(i) {
       x.sm <- smoothed.expression.matrices[[i]]
       scoreSmoothing(x = x.sm, method = autoAlphaMethod, is.counts = is.counts, dimReduceFlavor = autoAlphaDimReduceFlavor, 
           ...)
   }))
7: BiocParallel::bplapply(seq_len(length(smoothed.expression.matrices)), function(i) {
       x.sm <- smoothed.expression.matrices[[i]]
       scoreSmoothing(x = x.sm, method = autoAlphaMethod, is.counts = is.counts, dimReduceFlavor = autoAlphaDimReduceFlavor, 
           ...)
   })
8: BiocParallel::bplapply(seq_len(length(smoothed.expression.matrices)), function(i) {
       x.sm <- smoothed.expression.matrices[[i]]
       scoreSmoothing(x = x.sm, method = autoAlphaMethod, is.counts = is.counts, dimReduceFlavor = autoAlphaDimReduceFlavor, 
           ...)
   })
9: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
10: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
11: bploop(structure(list(), class = "lapply"), X, lapply, ARGFUN, BPPARAM)
12: bploop.lapply(structure(list(), class = "lapply"), X, lapply, ARGFUN, BPPARAM)

thread_monitor No such process in pthread_detach
thread_monitor No such process in pthread_detach
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 13 SKIPPED: 0 FAILED: 1
1. Error: netSmooth accepts SingleCellExperiment (@test_netsmooth.R#11) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
netSmooth	0.024	0.002	0.026
pickDimReduction	4.532	0.105	4.655
robustClusters	4.890	0.249	5.201