VJ Carey
| Snapshot Date: 2019-09-19 17:00:30 -0400 (Thu, 19 Sep 2019) |
| URL: https://git.bioconductor.org/packages/BiocSklearn |
| Branch: master |
| Last Commit: d71be87 |
| Last Changed Date: 2019-05-02 12:14:59 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2019-09-20 12:32:03 -0400 (Fri, 20 Sep 2019).
| Package 157/1770 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocSklearn 1.7.0 VJ Carey
| malbec1 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BiocSklearn |
| Version: 1.7.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BiocSklearn_1.7.0.tar.gz |
| StartedAt: 2019-09-20 01:23:07 -0400 (Fri, 20 Sep 2019) |
| EndedAt: 2019-09-20 01:26:08 -0400 (Fri, 20 Sep 2019) |
| EllapsedTime: 180.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocSklearn.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BiocSklearn_1.7.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BiocSklearn.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocSklearn/DESCRIPTION' ... OK
* this is package 'BiocSklearn' version '1.7.0'
* 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:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BiocSklearn' can be installed ... OK
* checking installed package size ... NOTE
installed size is 32.6Mb
sub-directories of 1Mb or more:
ban_6_17 29.1Mb
hdf5 3.1Mb
* 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 ... 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
H5matref 5.53 0.38 15.48
skIncrPPCA 4.08 0.67 5.44
* 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:
> test_check("BiocSklearn")
Loading required package: BiocSklearn
Loading required package: reticulate
Loading required package: knitr
checking python library availability...
done.
-- 1. Failure: pyobj, skPCA, getTransformed work (@test_bcsk.R#31) ------------
all.equal(class(pp), clpca) isn't true.
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: pyobj, skPCA, getTransformed work (@test_bcsk.R#31)
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
'C:/Users/biocbuild/bbs-3.10-bioc/meat/BiocSklearn.Rcheck/00check.log'
for details.
BiocSklearn.Rcheck/00install.out
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiocSklearn
###
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* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
* installing *source* package 'BiocSklearn' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocSklearn'
finding HTML links ... done
H5matref html
SkDecomp-class html
SklearnEls html
h5mat html
skIncrPCA html
skIncrPPCA html
skKMeans html
skPCA html
skPartialPCA_step 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
* DONE (BiocSklearn)
Making 'packages.html' ... done
BiocSklearn.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-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(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
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
>
> test_check("BiocSklearn")
Loading required package: BiocSklearn
Loading required package: reticulate
Loading required package: knitr
checking python library availability...
done.
-- 1. Failure: pyobj, skPCA, getTransformed work (@test_bcsk.R#31) ------------
all.equal(class(pp), clpca) isn't true.
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: pyobj, skPCA, getTransformed work (@test_bcsk.R#31)
Error: testthat unit tests failed
Execution halted
BiocSklearn.Rcheck/BiocSklearn-Ex.timings
| name | user | system | elapsed | |
| H5matref | 5.53 | 0.38 | 15.48 | |
| SklearnEls | 0.02 | 0.00 | 0.02 | |
| h5mat | 0.02 | 0.00 | 0.01 | |
| skIncrPCA | 0.03 | 0.00 | 0.05 | |
| skIncrPPCA | 4.08 | 0.67 | 5.44 | |
| skKMeans | 0.17 | 0.00 | 0.29 | |
| skPCA | 0.02 | 0.00 | 0.02 | |
| skPartialPCA_step | 0.04 | 0.02 | 0.06 | |