| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:36:39 -0400 (Tue, 09 Apr 2019).
| Package 818/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iSEE 1.3.8 Charlotte Soneson
| 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 | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: iSEE |
| Version: 1.3.8 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_1.3.8.tar.gz |
| StartedAt: 2019-04-09 01:42:27 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:49:03 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 395.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: iSEE.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:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_1.3.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/iSEE.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 ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘1.3.8’
* 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 ‘iSEE’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSEE 11.417 0.432 11.905
annotateEnsembl 8.881 0.320 9.257
synchronizeAssays 8.543 0.426 9.033
modeGating 7.940 0.224 8.213
annotateEntrez 6.368 0.211 6.599
isColorMapCompatible 4.945 0.282 5.259
* 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:
global_discrete(1)
global_continuous(1)
── 1. Error: onLoad works (@test_zzz.R#7) ─────────────────────────────────────
invalid 'path' argument
1: normalizePath(shiny:::.globals$resources[["iSEE"]][["directoryPath"]]) at testthat/test_zzz.R:7
2: path.expand(path)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1128 SKIPPED: 2 FAILED: 1
1. Error: onLoad works (@test_zzz.R#7)
Error: testthat unit tests failed
In addition: Warning message:
In .local(object, ...) : using library sizes as size factors
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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/iSEE.Rcheck/00check.log’
for details.
iSEE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iSEE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘iSEE’ ... ** 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 (iSEE)
iSEE.Rcheck/tests/testthat.Rout.fail
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(iSEE)
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: SingleCellExperiment
>
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
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
Class: ExperimentColorMap
assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm
colData(1): passes_qc_checks_s
rowData(0):
all_discrete(0):
all_continuous(0):
global_discrete(1)
global_continuous(1)
── 1. Error: onLoad works (@test_zzz.R#7) ─────────────────────────────────────
invalid 'path' argument
1: normalizePath(shiny:::.globals$resources[["iSEE"]][["directoryPath"]]) at testthat/test_zzz.R:7
2: path.expand(path)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1128 SKIPPED: 2 FAILED: 1
1. Error: onLoad works (@test_zzz.R#7)
Error: testthat unit tests failed
In addition: Warning message:
In .local(object, ...) : using library sizes as size factors
Execution halted
iSEE.Rcheck/iSEE-Ex.timings
| name | user | system | elapsed | |
| ExperimentColorMap-class | 0.139 | 0.023 | 0.163 | |
| annotateEnsembl | 8.881 | 0.320 | 9.257 | |
| annotateEntrez | 6.368 | 0.211 | 6.599 | |
| availablePanelTypes | 0.000 | 0.000 | 0.001 | |
| colDataPlotDefaults | 0.848 | 0.034 | 0.885 | |
| colStatTableDefaults | 0.111 | 0.003 | 0.114 | |
| customDataPlotDefaults | 0.131 | 0.011 | 0.142 | |
| customStatTableDefaults | 0.111 | 0.001 | 0.112 | |
| featAssayPlotDefaults | 0.319 | 0.002 | 0.322 | |
| heatMapPlotDefaults | 0.196 | 0.002 | 0.199 | |
| iSEE | 11.417 | 0.432 | 11.905 | |
| isColorMapCompatible | 4.945 | 0.282 | 5.259 | |
| jitterPoints | 0.105 | 0.005 | 0.111 | |
| lassoPoints | 0.007 | 0.001 | 0.007 | |
| modeGating | 7.940 | 0.224 | 8.213 | |
| pointDefaults | 0.549 | 0.003 | 0.554 | |
| redDimPlotDefaults | 0.374 | 0.003 | 0.380 | |
| rowDataPlotDefaults | 0.334 | 0.002 | 0.337 | |
| rowStatTableDefaults | 0.154 | 0.002 | 0.156 | |
| sampAssayPlotDefaults | 0.331 | 0.002 | 0.334 | |
| selectDefaults | 0.384 | 0.002 | 0.387 | |
| subsetPointsByGrid | 0.160 | 0.024 | 0.183 | |
| synchronizeAssays | 8.543 | 0.426 | 9.033 | |