| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:12:10 -0400 (Wed, 16 Oct 2019).
| Package 1359/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| restfulSE 1.6.1 Shweta Gopaulakrishnan
| 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 |
| Package: restfulSE |
| Version: 1.6.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings restfulSE_1.6.1.tar.gz |
| StartedAt: 2019-10-16 04:27:47 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:39:02 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 674.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: restfulSE.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings restfulSE_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 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
‘/home/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck/00check.log’
for details.
restfulSE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL restfulSE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
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-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.
> 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
restfulSE.Rcheck/restfulSE-Ex.timings
| name | user | system | elapsed | |
| BQ3_Array | 0.001 | 0.000 | 0.000 | |
| BQ3_Source | 0 | 0 | 0 | |
| BQM_Array | 0 | 0 | 0 | |
| BQM_Source | 0 | 0 | 0 | |