| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:59 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bumphunter.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bumphunter_1.34.0.tar.gz |
| StartedAt: 2021-10-14 20:30:21 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:39:56 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 574.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bumphunter.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bumphunter.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bumphunter_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bumphunter 0.34 0.11 13.99
smoother 0.05 0.00 11.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bumphunter 0.97 0.02 14.30
smoother 0.07 0.00 12.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
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:
x
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
** running tests for arch 'x64' ...
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:
x
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: 2 ERRORs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck/00check.log'
for details.
bumphunter.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/bumphunter_1.34.0.tar.gz && rm -rf bumphunter.buildbin-libdir && mkdir bumphunter.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bumphunter.buildbin-libdir bumphunter_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL bumphunter_1.34.0.zip && rm bumphunter_1.34.0.tar.gz bumphunter_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
47 2274k 47 1084k 0 0 1386k 0 0:00:01 --:--:-- 0:00:01 1385k
100 2274k 100 2274k 0 0 1748k 0 0:00:01 0:00:01 --:--:-- 1749k
install for i386
* 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
converting help for package 'bumphunter'
finding HTML links ... done
TT html
annotateNearest html
annotateTranscripts html
bumphunter html
clusterMaker html
dummyData html
getSegments html
locfitByCluster html
loessByCluster html
matchGenes html
regionFinder html
runmedByCluster html
smoother html
** 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
install for x64
* installing *source* package 'bumphunter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bumphunter' as bumphunter_1.34.0.zip
* DONE (bumphunter)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'bumphunter' successfully unpacked and MD5 sums checked
|
bumphunter.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: 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.
[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 20:36:54 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
13.01 0.82 42.81
|
bumphunter.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: 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.
[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 20:38:46 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
15.79 0.48 48.18
|
|
bumphunter.Rcheck/tests_i386/test-all.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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')
> 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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:
x
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/tests_x64/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-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')
> 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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:
x
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
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bumphunter.Rcheck/examples_i386/bumphunter-Ex.timings
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bumphunter.Rcheck/examples_x64/bumphunter-Ex.timings
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