| Back to Multiple platform build/check report for BioC 3.11 (small subset of software packages ONLY) |
This page was generated on 2020-01-24 03:57:03 -0500 (Fri, 24 Jan 2020).
| Package 6/41 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| AnnotationHub 2.19.5 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ ERROR ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped |
| Package: AnnotationHub |
| Version: 2.19.5 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings AnnotationHub_2.19.5.tar.gz |
| StartedAt: 2020-01-24 03:01:50 -0500 (Fri, 24 Jan 2020) |
| EndedAt: 2020-01-24 03:06:04 -0500 (Fri, 24 Jan 2020) |
| EllapsedTime: 253.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AnnotationHub.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings AnnotationHub_2.19.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/AnnotationHub.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHub’ version ‘2.19.5’
* 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 ‘AnnotationHub’ 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 ... WARNING
'::' or ':::' import not declared from: ‘ensembldb’
Unexported objects imported by ':::' calls:
‘BiocFileCache:::.get_tbl_rid’ ‘BiocManager:::.version_bioc’
‘BiocManager:::isDevel’
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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnotationHub-class 62.009 0.891 64.934
* 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:
FALSE
Test files with failing tests
test_tidyGRanges.R
test_tidyGRanges
Error in BiocGenerics:::testPackage("AnnotationHub") :
unit tests failed for package AnnotationHub
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'xxx_foo'
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
‘/home/biocbuild/bbs-3.11-bioc-testing/meat/AnnotationHub.Rcheck/00check.log’
for details.
AnnotationHub.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL AnnotationHub ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’ * installing *source* package ‘AnnotationHub’ ... ** using staged installation ** R ** 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 (AnnotationHub)
AnnotationHub.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2019-12-14 r77569) -- "Unsuffered Consequences"
Copyright (C) 2019 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("AnnotationHub")
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, which.max, which.min
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
snapshotDate(): 2020-01-09
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Timing stopped at: 2.638 0.016 3.594
Error in checkIdentical(setNames(rep("calJac3", 5), chr), GenomeInfoDb::genome(gr2)) :
FALSE
In addition: Warning messages:
1: call dbDisconnect() when finished working with a connection
2: download failed
hub path: 'bogus/url'
cache resource: 'AHInvalid : 5012'
reason: all(rtype == "web" | file.exists(fpath)) is not TRUE
require("xxx_foo")
RUNIT TEST PROTOCOL -- Fri Jan 24 03:06:01 2020
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 1
1 Test Suite :
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 1 failure
FAILURE in test_tidyGRanges: Error in checkIdentical(setNames(rep("calJac3", 5), chr), GenomeInfoDb::genome(gr2)) :
FALSE
Test files with failing tests
test_tidyGRanges.R
test_tidyGRanges
Error in BiocGenerics:::testPackage("AnnotationHub") :
unit tests failed for package AnnotationHub
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'xxx_foo'
Execution halted
AnnotationHub.Rcheck/AnnotationHub-Ex.timings
| name | user | system | elapsed | |
| AnnotationHub-class | 62.009 | 0.891 | 64.934 | |
| AnnotationHub-package | 0.001 | 0.000 | 0.000 | |
| Hub-utils | 0 | 0 | 0 | |
| convertHub | 0 | 0 | 0 | |
| getAnnotationHubOption | 0 | 0 | 0 | |
| utils | 0.002 | 0.000 | 0.002 | |