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This page was generated on 2017-10-18 14:35:16 -0400 (Wed, 18 Oct 2017).
| Package 284/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coseq 1.0.1 Andrea Rau
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: coseq |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coseq_1.0.1.tar.gz |
| StartedAt: 2017-10-18 02:12:57 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 02:16:56 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 239.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: coseq.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coseq_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/coseq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coseq’ version ‘1.0.1’
* 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 ‘coseq’ 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareARI 9.047 0.096 9.432
* 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:
****************************************
1. Failure: compareARI (@test-coseq.R#45) --------------------------------------
compareARI(obj2) did not throw an error.
****************************************
coseq analysis: Normal approach & logMedianRef transformation
K = 2 to 4
****************************************
testthat results ================================================================
OK: 30 SKIPPED: 0 FAILED: 1
1. Failure: compareARI (@test-coseq.R#45)
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
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/coseq.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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("coseq")
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
> test_check("coseq")
****************************************
coseq analysis: kmeans approach & logclr transformation
K = -3 to -3
****************************************
****************************************
coseq analysis: kmeans approach & logclr transformation
K = -0.4816474 to 1.805098
****************************************
****************************************
coseq analysis: kmeans approach & logclr transformation
K = -3 to 3
****************************************
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 0 to 3
****************************************
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 1.5 to 5.2
****************************************
****************************************
coseq analysis: Gamma approach & logclr transformation
K = 2 to 4
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4
****************************************
****************************************
coseq analysis: Normal approach & none transformation
K = 2 to 4
****************************************
1. Failure: compareARI (@test-coseq.R#45) --------------------------------------
compareARI(obj2) did not throw an error.
****************************************
coseq analysis: Normal approach & logMedianRef transformation
K = 2 to 4
****************************************
testthat results ================================================================
OK: 30 SKIPPED: 0 FAILED: 1
1. Failure: compareARI (@test-coseq.R#45)
Error: testthat unit tests failed
Execution halted
coseq.Rcheck/00install.out:
* installing *source* package ‘coseq’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (coseq)
coseq.Rcheck/coseq-Ex.timings:
| name | user | system | elapsed | |
| NormMixClus | 1.160 | 0.034 | 1.221 | |
| NormMixClusK | 0.647 | 0.004 | 0.662 | |
| NormMixParam | 0.143 | 0.002 | 0.148 | |
| clusterEntropy | 0.001 | 0.000 | 0.002 | |
| clusterInertia | 0.742 | 0.014 | 0.783 | |
| compareARI | 9.047 | 0.096 | 9.432 | |
| compareICL | 4.603 | 0.044 | 4.842 | |
| coseq-package | 3.472 | 0.027 | 3.578 | |
| coseq | 3.460 | 0.027 | 3.600 | |
| coseqHelpers | 3.986 | 0.027 | 4.120 | |
| coseqRun | 1.276 | 0.010 | 1.329 | |
| kmeansProbaPost | 0.044 | 0.000 | 0.046 | |
| matchContTable | 0.005 | 0.000 | 0.005 | |
| plot | 3.326 | 0.027 | 3.465 | |
| summary | 3.925 | 0.028 | 4.076 | |
| transformRNAseq | 0.008 | 0.001 | 0.008 | |