| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:28:54 -0400 (Wed, 17 Oct 2018).
| Package 1068/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pbcmc 1.8.0 Cristobal Fresno
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: pbcmc |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pbcmc_1.8.0.tar.gz |
| StartedAt: 2018-10-16 02:35:24 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:37:28 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 123.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pbcmc.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pbcmc_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/pbcmc.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pbcmc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pbcmc’ version ‘1.8.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pbcmc’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
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
‘/home/biocbuild/bbs-3.7-bioc/meat/pbcmc.Rcheck/00check.log’
for details.
pbcmc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pbcmc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘pbcmc’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘pbcmc’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘pbcmc’ * DONE (pbcmc)
pbcmc.Rcheck/tests/runTests.Rout.fail
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> BiocGenerics:::testPackage("pbcmc")
Package 'mclust' version 5.4.1
Type 'citation("mclust")' for citing this R package in publications.
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 object is masked from 'package:limma':
plotMA
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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Loading required namespace: breastCancerNKI
Timing stopped at: 1.372 0.02 1.392
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Timing stopped at: 1.104 0.036 1.142
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
RUNIT TEST PROTOCOL -- Tue Oct 16 02:37:25 2018
***********************************************
Number of test functions: 14
Number of errors: 0
Number of failures: 2
1 Test Suite :
pbcmc RUnit Tests - 14 test functions, 0 errors, 2 failures
FAILURE in test_databaseReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
Execution halted
pbcmc.Rcheck/pbcmc-Ex.timings
| name | user | system | elapsed | |
| MolecularPermutationClassifierConstructor | 0.984 | 0.028 | 1.113 | |
| MolecularPermutationClassifierGenerics | 0.524 | 0.388 | 0.658 | |
| MolecularPermutationClassifierGetseters | 0.052 | 0.000 | 0.053 | |
| MolecularPermutationClassifierShow | 0.040 | 0.004 | 0.044 | |
| PAM50-class | 2.504 | 0.336 | 2.565 | |
| PAM50Classify | 0.044 | 0.004 | 0.051 | |
| PAM50Constructor | 0.880 | 0.032 | 0.914 | |
| PAM50Filtrate | 0.844 | 0.052 | 0.898 | |
| PAM50Permutate | 0.336 | 0.184 | 0.398 | |
| PAM50SubjectReport | 2.340 | 0.168 | 2.244 | |
| PAM50Subtype | 0.052 | 0.004 | 0.056 | |