| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:37:07 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iSEE_1.3.8.tar.gz |
| StartedAt: 2019-04-09 03:42:21 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:52:32 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 610.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: iSEE.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iSEE_1.3.8.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/iSEE.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSEE 12.04 0.23 12.28
annotateEnsembl 11.00 0.22 11.79
modeGating 8.20 0.33 8.53
synchronizeAssays 7.97 0.39 8.39
annotateEntrez 6.23 0.36 6.60
isColorMapCompatible 5.83 0.22 6.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSEE 11.35 0.35 11.70
annotateEnsembl 9.17 0.23 9.40
synchronizeAssays 7.66 0.40 8.06
modeGating 7.45 0.42 7.88
annotateEntrez 5.85 0.19 6.03
isColorMapCompatible 5.25 0.32 5.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
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$resources[["iSEE"]][["directoryPath"]]) at testthat/test_zzz.R:7
2: path.expand(path)
== testthat results ===========================================================
OK: 1128 SKIPPED: 2 FAILED: 1
1. Error: onLoad works (@test_zzz.R#7)
Error: testthat unit tests failed
In addition: Warning message:
In .local(object, ...) : using library sizes as size factors
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
global_discrete(1)
global_continuous(1)
-- 1. Error: onLoad works (@test_zzz.R#7) -------------------------------------
invalid 'path' argument
1: normalizePath(shiny:::.globals$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: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/iSEE.Rcheck/00check.log'
for details.
iSEE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/iSEE_1.3.8.tar.gz && rm -rf iSEE.buildbin-libdir && mkdir iSEE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iSEE.buildbin-libdir iSEE_1.3.8.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL iSEE_1.3.8.zip && rm iSEE_1.3.8.tar.gz iSEE_1.3.8.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 438k 100 438k 0 0 6084k 0 --:--:-- --:--:-- --:--:-- 6849k
install for i386
* installing *source* package 'iSEE' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'iSEE'
finding HTML links ... done
ExperimentColorMap-class html
annotateEnsembl html
finding level-2 HTML links ... done
annotateEntrez html
availablePanelTypes html
colDataPlotDefaults html
colStatTableDefaults html
customDataPlotDefaults html
customStatTableDefaults html
featAssayPlotDefaults html
heatMapPlotDefaults html
iSEE-pkg html
iSEE html
isColorMapCompatible html
jitterPoints html
lassoPoints html
modeGating html
pointDefaults html
prepareSpeechRecognition html
redDimPlotDefaults html
rowDataPlotDefaults html
rowStatTableDefaults html
sampAssayPlotDefaults html
selectDefaults html
subsetPointsByGrid html
synchronizeAssays html
** 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
install for x64
* installing *source* package 'iSEE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iSEE' as iSEE_1.3.8.zip
* DONE (iSEE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'iSEE' successfully unpacked and MD5 sums checked
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iSEE.Rcheck/tests_i386/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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/tests_x64/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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iSEE.Rcheck/examples_i386/iSEE-Ex.timings
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iSEE.Rcheck/examples_x64/iSEE-Ex.timings
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