| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the bumphunter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bumphunter.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 223/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bumphunter 1.34.0 (landing page) Rafael A. Irizarry
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: bumphunter |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.34.0.tar.gz |
| StartedAt: 2021-10-14 16:58:58 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:06:48 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 469.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bumphunter.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach',
'iterators', 'parallel', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
bootstraps
* 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 LazyData ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bumphunter 4.002 2.315 3.481
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
Error in `download.file(resource(con), destfile)`: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
Backtrace:
█
1. ├─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz") test_annotation.R:99:0
2. └─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz")
3. ├─BiocIO::import(FileForFormat(con), ...)
4. └─BiocIO::import(FileForFormat(con), ...)
5. ├─BiocIO::import(con, ...)
6. └─rtracklayer::import(con, ...)
7. └─rtracklayer:::.local(con, format, text, ...)
8. └─utils::download.file(resource(con), destfile)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
Error: Test failures
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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck/00check.log’
for details.
bumphunter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bumphunter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘bumphunter’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bumphunter)
bumphunter.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> require("bumphunter") || stop("unable to load bumphunter")
Loading required package: bumphunter
Loading required package: S4Vectors
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, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
[1] TRUE
> BiocGenerics:::testPackage("bumphunter")
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
Loading required package: doParallel
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelMC, version: 1.0.16).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelSNOW, version: 1.0.16).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
RUNIT TEST PROTOCOL -- Thu Oct 14 17:04:28 2021
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
bumphunter RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
23.850 2.339 42.013
bumphunter.Rcheck/tests/test-all.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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')
> test_check('bumphunter')
Loading required package: bumphunter
Loading required package: S4Vectors
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, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_annotation.R:99:1): (code run outside of `test_that()`) ─────────
Error in `download.file(resource(con), destfile)`: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
Backtrace:
█
1. ├─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz") test_annotation.R:99:0
2. └─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz")
3. ├─BiocIO::import(FileForFormat(con), ...)
4. └─BiocIO::import(FileForFormat(con), ...)
5. ├─BiocIO::import(con, ...)
6. └─rtracklayer::import(con, ...)
7. └─rtracklayer:::.local(con, format, text, ...)
8. └─utils::download.file(resource(con), destfile)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted
bumphunter.Rcheck/bumphunter-Ex.timings
| name | user | system | elapsed | |
| annotateNearest | 1.031 | 0.104 | 1.136 | |
| annotateTranscripts | 0 | 0 | 0 | |
| bumphunter | 4.002 | 2.315 | 3.481 | |
| clusterMaker | 0.013 | 0.002 | 0.015 | |
| dummyData | 0.004 | 0.001 | 0.004 | |
| getSegments | 0.022 | 0.004 | 0.026 | |
| locfitByCluster | 0.031 | 0.006 | 0.036 | |
| loessByCluster | 0.291 | 0.031 | 0.322 | |
| matchGenes | 0.000 | 0.001 | 0.000 | |
| regionFinder | 0.024 | 0.003 | 0.027 | |
| runmedByCluster | 0.003 | 0.001 | 0.004 | |
| smoother | 0.108 | 0.094 | 0.174 | |