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This page was generated on 2017-10-18 14:26:48 -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: rm -rf coseq.buildbin-libdir coseq.Rcheck && mkdir coseq.buildbin-libdir coseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coseq.buildbin-libdir coseq_1.0.1.tar.gz >coseq.Rcheck\00install.out 2>&1 && cp coseq.Rcheck\00install.out coseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coseq.buildbin-libdir --install="check:coseq-install.out" --force-multiarch --no-vignettes --timings coseq_1.0.1.tar.gz |
| StartedAt: 2017-10-17 23:02:36 -0400 (Tue, 17 Oct 2017) |
| EndedAt: 2017-10-17 23:08:48 -0400 (Tue, 17 Oct 2017) |
| EllapsedTime: 371.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: coseq.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf coseq.buildbin-libdir coseq.Rcheck && mkdir coseq.buildbin-libdir coseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coseq.buildbin-libdir coseq_1.0.1.tar.gz >coseq.Rcheck\00install.out 2>&1 && cp coseq.Rcheck\00install.out coseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coseq.buildbin-libdir --install="check:coseq-install.out" --force-multiarch --no-vignettes --timings coseq_1.0.1.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/coseq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareARI 6.12 0.03 6.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareARI 9.30 0.01 9.31
compareICL 5.81 0.02 5.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
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
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/coseq.Rcheck/00check.log'
for details.
testthat.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("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
testthat.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("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:
install for i386 * 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 install for x64 * installing *source* package 'coseq' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'coseq' as coseq_1.0.1.zip * DONE (coseq)
coseq.Rcheck/examples_i386/coseq-Ex.timings:
| name | user | system | elapsed | |
| NormMixClus | 0.81 | 0.05 | 0.86 | |
| NormMixClusK | 0.49 | 0.00 | 0.49 | |
| NormMixParam | 0.12 | 0.00 | 0.12 | |
| clusterEntropy | 0 | 0 | 0 | |
| clusterInertia | 0.58 | 0.02 | 0.60 | |
| compareARI | 6.12 | 0.03 | 6.15 | |
| compareICL | 3.35 | 0.06 | 3.41 | |
| coseq-package | 2.61 | 0.02 | 2.62 | |
| coseq | 2.73 | 0.01 | 2.75 | |
| coseqHelpers | 2.69 | 0.00 | 2.69 | |
| coseqRun | 0.97 | 0.00 | 0.97 | |
| kmeansProbaPost | 0.01 | 0.00 | 0.01 | |
| matchContTable | 0.02 | 0.00 | 0.02 | |
| plot | 2.69 | 0.03 | 2.72 | |
| summary | 3.18 | 0.00 | 3.19 | |
| transformRNAseq | 0 | 0 | 0 | |
coseq.Rcheck/examples_x64/coseq-Ex.timings:
| name | user | system | elapsed | |
| NormMixClus | 1.46 | 0.03 | 1.53 | |
| NormMixClusK | 0.72 | 0.00 | 0.72 | |
| NormMixParam | 0.18 | 0.00 | 0.18 | |
| clusterEntropy | 0 | 0 | 0 | |
| clusterInertia | 0.64 | 0.02 | 0.65 | |
| compareARI | 9.30 | 0.01 | 9.31 | |
| compareICL | 5.81 | 0.02 | 5.83 | |
| coseq-package | 3.66 | 0.03 | 3.69 | |
| coseq | 3.73 | 0.00 | 3.73 | |
| coseqHelpers | 3.96 | 0.00 | 3.97 | |
| coseqRun | 1.32 | 0.00 | 1.33 | |
| kmeansProbaPost | 0.04 | 0.00 | 0.03 | |
| matchContTable | 0.01 | 0.00 | 0.02 | |
| plot | 3.95 | 0.00 | 3.95 | |
| summary | 3.75 | 0.00 | 3.75 | |
| transformRNAseq | 0 | 0 | 0 | |