| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:59:34 -0400 (Tue, 16 Apr 2019).
| Package 1131/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Cristobal Fresno
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | ERROR | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: pbcmc |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pbcmc_1.10.1.tar.gz |
| StartedAt: 2019-04-16 01:48:43 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:51:51 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 187.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pbcmc.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pbcmc_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.1’
* 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 ‘pbcmc’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... 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, 1 WARNING
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00check.log’
for details.
pbcmc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pbcmc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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’ Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor version 3.9 * DONE (pbcmc)
pbcmc.Rcheck/tests/runTests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("pbcmc")
Package 'mclust' version 5.4.3
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: 2.037 0.13 2.176
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.
In addition: Warning message:
Package 'pbcmc' is deprecated and will be removed from Bioconductor
version 3.9
Timing stopped at: 1.486 0.122 1.615
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 Apr 16 01:51:45 2019
***********************************************
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 | 1.132 | 0.062 | 1.228 | |
| MolecularPermutationClassifierGenerics | 0.955 | 0.596 | 0.857 | |
| MolecularPermutationClassifierGetseters | 0.060 | 0.018 | 0.079 | |
| MolecularPermutationClassifierShow | 0.065 | 0.016 | 0.082 | |
| PAM50-class | 4.119 | 0.740 | 4.248 | |
| PAM50Classify | 0.070 | 0.008 | 0.080 | |
| PAM50Constructor | 0.989 | 0.126 | 1.118 | |
| PAM50Filtrate | 1.037 | 0.083 | 1.131 | |
| PAM50Permutate | 0.861 | 0.571 | 0.683 | |
| PAM50SubjectReport | 2.819 | 0.211 | 3.056 | |
| PAM50Subtype | 0.057 | 0.007 | 0.064 | |