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CHECK report for ensembldb on malbec2

This page was generated on 2018-10-17 08:27:22 -0400 (Wed, 17 Oct 2018).

Package 449/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 2.4.1
Johannes Rainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ensembldb
Branch: RELEASE_3_7
Last Commit: b5b6b94
Last Changed Date: 2018-05-04 09:28:27 -0400 (Fri, 04 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ensembldb
Version: 2.4.1
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ensembldb_2.4.1.tar.gz
StartedAt: 2018-10-16 00:10:19 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:17:29 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 430.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: ensembldb.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ensembldb_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ensembldb.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.4.1’
* 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 ‘ensembldb’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Filter-classes      2.360  1.088   5.202
EnsDb-AnnotationDbi 3.036  0.352   6.375
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: In getClassDef(class1) :
    closing unused connection 9 (ftp://ftp.ensemblgenomes.org/pub/release-21/plants/mysql/)
  5: In getClassDef(class1) :
    closing unused connection 8 (ftp://ftp.ensemblgenomes.org/pub/release-21/metazoa/mysql/)
  6: In getClassDef(class1) :
    closing unused connection 7 (ftp://ftp.ensemblgenomes.org/pub/release-21/fungi/mysql/)
  7: In getClassDef(class1) :
    closing unused connection 6 (ftp://ftp.ensemblgenomes.org/pub/release-21/bacteria/mysql/)
  8: In getClassDef(class1) :
    closing unused connection 5 (ftp://ftp.ensembl.org/pub/release-77/mysql/)
  9: In getClassDef(class1) :
    closing unused connection 4 (ftp://ftp.ensembl.org/pub/release-61/mysql/)
  10: In getClassDef(class1) :
    closing unused connection 3 (ftp://ftp.ensembl.org/pub/release-85/mysql/)
  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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/ensembldb.Rcheck/00check.log’
for details.

Installation output

ensembldb.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ensembldb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ensembldb’ ...
** 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
* DONE (ensembldb)

Tests output

ensembldb.Rcheck/tests/testthat.Rout.fail


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> library(testthat)
> library(ensembldb)
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, 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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

The following object is masked from 'package:testthat':

    not


Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter

> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
> 
> test_check("ensembldb")
Creating package in /tmp/Rtmp1BjqoZ/EnsDb.Hsapiens.v75 

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (0) identical, (4045) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK

Comparing metadata:
 Ensembl versions match.
 Genome builds match.
 All differences: <name>: <value x> != <value y>
  -  Creation time : Tue Oct 16 00:14:39 2018  !=  Tue Oct 16 00:14:26 2018 
  -  source_file : Devosia_geojensis.ASM96941v1.32.gtf.gz  !=  Devosia_geojensis.ASM96941v1.32.gff3.gz 
Done. Result: NOTE

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (0) identical, (4045) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK
Error in readLines(curl(my_url)) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
In addition: There were 12 warnings (use warnings() to see them)
── 1. Error: getEnsemblMysqlUrl works (@test_functions-create-EnsDb.R#195)  ────
No database matching 'fusarium_oxysporum_core_21' found in Ensembl's ftp server
1: ensembldb:::.getEnsemblMysqlUrl(type = "ensemblgenomes", organism = "fusarium_oxysporum", 
       ensembl = 21) at testthat/test_functions-create-EnsDb.R:195
2: stop("No database matching '", db_name, "' found in Ensembl's", " ftp server")


Comparing protein data:
 protein IDs: (103725) common, (0) only in x, (0) only in y.
 Transcript IDs: (103725) identical, (0) different.
 Protein sequence: (103725) identical, (0) different.
Done. Result: OK
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1346 SKIPPED: 3 FAILED: 1
1. Error: getEnsemblMysqlUrl works (@test_functions-create-EnsDb.R#195) 

Error: testthat unit tests failed
In addition: Warning messages:
1: In getClassDef(class1) :
  closing unused connection 12 (ftp://ftp.ensembl.org/pub/release-86/mysql/)
2: In getClassDef(class1) :
  closing unused connection 11 (ftp://ftp.ensembl.org/pub/)
3: In getClassDef(class1) :
  closing unused connection 10 (ftp://ftp.ensemblgenomes.org/pub/release-21/protists/mysql/)
4: In getClassDef(class1) :
  closing unused connection 9 (ftp://ftp.ensemblgenomes.org/pub/release-21/plants/mysql/)
5: In getClassDef(class1) :
  closing unused connection 8 (ftp://ftp.ensemblgenomes.org/pub/release-21/metazoa/mysql/)
6: In getClassDef(class1) :
  closing unused connection 7 (ftp://ftp.ensemblgenomes.org/pub/release-21/fungi/mysql/)
7: In getClassDef(class1) :
  closing unused connection 6 (ftp://ftp.ensemblgenomes.org/pub/release-21/bacteria/mysql/)
8: In getClassDef(class1) :
  closing unused connection 5 (ftp://ftp.ensembl.org/pub/release-77/mysql/)
9: In getClassDef(class1) :
  closing unused connection 4 (ftp://ftp.ensembl.org/pub/release-61/mysql/)
10: In getClassDef(class1) :
  closing unused connection 3 (ftp://ftp.ensembl.org/pub/release-85/mysql/)
Execution halted

Example timings

ensembldb.Rcheck/ensembldb-Ex.timings

nameusersystemelapsed
EnsDb-AnnotationDbi3.0360.3526.375
EnsDb-class1.0720.0921.183
EnsDb-exonsBy1.6760.3442.903
EnsDb-lengths1.4000.0721.473
EnsDb-seqlevels0.0360.0080.043
EnsDb-sequences0.0080.0000.008
EnsDb-utils0.1760.0000.179
EnsDb1.1680.0521.221
Filter-classes2.3601.0885.202
ProteinFunctionality0.3240.1480.474
cdsToTranscript1.1560.0441.252
convertFilter0.0200.0000.018
genomeToProtein3.1080.1003.210
genomeToTranscript4.3920.0084.404
global-filters0.0920.0000.092
hasProteinData-EnsDb-method0.0120.0000.011
listEnsDbs0.0040.0000.001
makeEnsemblDbPackage0.6400.0000.663
proteinToGenome1.7800.1162.189
proteinToTranscript0.8840.1841.070
transcriptToCds0.3680.0000.367
transcriptToGenome0.7560.0000.757
transcriptToProtein1.5960.2321.848
useMySQL-EnsDb-method0.0080.0000.009