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CHECK report for restfulSE on celaya2

This page was generated on 2019-10-16 13:01:01 -0400 (Wed, 16 Oct 2019).

Package 1359/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
restfulSE 1.6.1
Shweta Gopaulakrishnan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/restfulSE
Branch: RELEASE_3_9
Last Commit: 0d26e30
Last Changed Date: 2019-08-19 15:46:28 -0400 (Mon, 19 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: restfulSE
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings restfulSE_1.6.1.tar.gz
StartedAt: 2019-10-16 06:10:34 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:19:46 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 551.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: restfulSE.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings restfulSE_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘restfulSE/DESCRIPTION’ ... OK
* this is package ‘restfulSE’ version ‘1.6.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘restfulSE’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BQ3_Source: no visible binding for global variable
  ‘SampleTypeLetterCode’
BQ3m2: no visible binding for global variable ‘SampleTypeLetterCode’
Undefined global functions or variables:
  SampleTypeLetterCode
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘restfulSE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ###   RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ###   .RESTfulSummarizedExperiment assay
> ###   assay,RESTfulSummarizedExperiment,missing-method
> 
> ### ** Examples
> 
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in transl(target) : 
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
Calls: H5S_source -> hsdsInfo -> hsdsInfo -> transl
Execution halted
* 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:
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
  1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
  2: hsdsInfo(tmp)
  3: hsdsInfo(tmp)
  4: transl(target)
  5: stop(paste("error: can't read JSON ", targ, sep = ""))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: H5S_source completes (@test_reSE.R#9) 
  2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
  3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 
  
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck/00check.log’
for details.

Installation output

restfulSE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL restfulSE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘restfulSE’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (restfulSE)

Tests output

restfulSE.Rcheck/tests/testthat.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(restfulSE)
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


> library(rhdf5client)
> 
> test_check("restfulSE")
── 1. Error: H5S_source completes (@test_reSE.R#9)  ────────────────────────────
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:9
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

── 2. Error: RESTfulSummarizedExperiment infrastructure works against server (@t
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:51
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

── 3. Error: dim compatibility check is sensitive (@test_reSE.R#121)  ──────────
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9) 
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 

Error: testthat unit tests failed
Execution halted

Example timings

restfulSE.Rcheck/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array0.0010.0010.001
BQ3_Source0.0010.0010.001
BQM_Array0.0020.0010.002
BQM_Source0.0010.0000.001