| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:06:42 -0400 (Tue, 09 Apr 2019).
| Package 279/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.23.0 Paolo Martini
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: clipper |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.23.0.tar.gz |
| StartedAt: 2019-04-09 00:44:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:00:35 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 944.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: clipper.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:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.23.0’
* 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 ‘clipper’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipperAllRoots 70.254 2.640 73.833
clipper 63.601 3.175 67.742
easyClip 49.524 2.096 54.585
cliqueMeanTest 50.583 0.851 51.649
cliqueMixedTest 49.215 1.536 50.957
cliquePairedTest 48.133 0.627 48.800
pathwayTest 46.501 1.037 47.546
cliqueVarianceTest 46.905 0.546 47.463
getGraphEntryGenes 42.656 0.501 47.384
deleteEdge 40.608 0.319 40.970
getJunctionTreePaths 40.226 0.571 43.110
* 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:
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
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-3.9-bioc/meat/clipper.Rcheck/00check.log’
for details.
clipper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clipper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘clipper’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** testing if installed package can be loaded from final location No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** testing if installed package keeps a record of temporary installation path * DONE (clipper)
clipper.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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("clipper")
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:Matrix':
colMeans, colSums, rowMeans, rowSums, which
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, 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
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Timing stopped at: 1.366 0.016 1.382
Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
RUNIT TEST PROTOCOL -- Tue Apr 9 01:00:28 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 1
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
Execution halted
clipper.Rcheck/clipper-Ex.timings
| name | user | system | elapsed | |
| clipper | 63.601 | 3.175 | 67.742 | |
| clipperAllRoots | 70.254 | 2.640 | 73.833 | |
| cliqueMeanTest | 50.583 | 0.851 | 51.649 | |
| cliqueMixedTest | 49.215 | 1.536 | 50.957 | |
| cliquePairedTest | 48.133 | 0.627 | 48.800 | |
| cliqueVarianceTest | 46.905 | 0.546 | 47.463 | |
| deleteEdge | 40.608 | 0.319 | 40.970 | |
| easyClip | 49.524 | 2.096 | 54.585 | |
| getGraphEntryGenes | 42.656 | 0.501 | 47.384 | |
| getJunctionTreePaths | 40.226 | 0.571 | 43.110 | |
| nameCliques | 0.001 | 0.000 | 0.000 | |
| pathwayTest | 46.501 | 1.037 | 47.546 | |
| plotInCytoscape | 0.000 | 0.001 | 0.000 | |
| prunePaths | 0.006 | 0.001 | 0.007 | |