| 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 18/41 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| ensembldb 2.11.3 Johannes Rainer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ OK ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped |
| Package: ensembldb |
| Version: 2.11.3 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ensembldb_2.11.3.tar.gz |
| StartedAt: 2020-01-24 03:15:09 -0500 (Fri, 24 Jan 2020) |
| EndedAt: 2020-01-24 03:26:08 -0500 (Fri, 24 Jan 2020) |
| EllapsedTime: 659.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ensembldb.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ensembldb_2.11.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/ensembldb.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 ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.11.3’
* 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 (user + system) or elapsed time > 5s
user system elapsed
Filter-classes 3.694 1.331 9.204
EnsDb-AnnotationDbi 3.673 0.475 8.045
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
ensembldb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’ * installing *source* package ‘ensembldb’ ... ** 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 (ensembldb)
ensembldb.Rcheck/tests/testthat.Rout
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.
> 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, 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
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")'.
Attaching package: 'GenomicFeatures'
The following object is masked from 'package:GenomeInfoDb':
getChromInfoFromUCSC
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/Rtmpid1z0f/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: (4045) identical, (0) 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 : Fri Jan 24 03:22:59 2020 != Fri Jan 24 03:22:50 2020
- 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: (4045) identical, (0) 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 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: 1449 | SKIPPED: 3 | WARNINGS: 82 | FAILED: 0 ]
There were 25 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
222.940 20.015 291.867
ensembldb.Rcheck/ensembldb-Ex.timings
| name | user | system | elapsed | |
| EnsDb-AnnotationDbi | 3.673 | 0.475 | 8.045 | |
| EnsDb-class | 2.729 | 0.108 | 3.175 | |
| EnsDb-exonsBy | 3.170 | 0.430 | 4.058 | |
| EnsDb-lengths | 1.537 | 0.120 | 1.657 | |
| EnsDb-seqlevels | 0.085 | 0.000 | 0.085 | |
| EnsDb-sequences | 0.019 | 0.000 | 0.019 | |
| EnsDb-utils | 0.382 | 0.000 | 0.381 | |
| EnsDb | 2.050 | 0.088 | 2.140 | |
| Filter-classes | 3.694 | 1.331 | 9.204 | |
| ProteinFunctionality | 0.085 | 0.029 | 0.117 | |
| cdsToTranscript | 2.617 | 0.008 | 2.899 | |
| convertFilter | 0.042 | 0.000 | 0.042 | |
| genomeToProtein | 3.123 | 0.019 | 3.142 | |
| genomeToTranscript | 2.636 | 0.064 | 2.700 | |
| global-filters | 0.204 | 0.000 | 0.204 | |
| hasProteinData-EnsDb-method | 0.028 | 0.000 | 0.028 | |
| listEnsDbs | 0.001 | 0.000 | 0.001 | |
| makeEnsemblDbPackage | 1.127 | 0.007 | 1.389 | |
| proteinToGenome | 3.644 | 0.069 | 3.946 | |
| proteinToTranscript | 1.387 | 0.052 | 1.538 | |
| transcriptToCds | 0.991 | 0.003 | 0.994 | |
| transcriptToGenome | 1.842 | 0.012 | 1.854 | |
| transcriptToProtein | 2.868 | 0.020 | 2.891 | |
| useMySQL-EnsDb-method | 0.02 | 0.00 | 0.02 | |