Back to "Blame Jeroen" build/check report for BioC 3.11

CHECK report for ensembldb on tokay2

This page was generated on 2020-04-15 03:20:14 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE ensembldb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 33/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 2.11.3
Johannes Rainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ensembldb
Branch: master
Last Commit: 514b9d3
Last Changed Date: 2020-01-22 10:20:06 -0400 (Wed, 22 Jan 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK 

Summary

Package: ensembldb
Version: 2.11.3
Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:ensembldb.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings ensembldb_2.11.3.tar.gz
StartedAt: 2020-04-14 22:35:08 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 23:02:21 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 1633.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ensembldb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:ensembldb.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings ensembldb_2.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/ensembldb.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Filter-classes      4.10   3.72  561.06
EnsDb-exonsBy       2.75   1.37   12.52
EnsDb-AnnotationDbi 2.70   0.83   16.90
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

Installation output

ensembldb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/ensembldb_2.11.3.tar.gz && rm -rf ensembldb.buildbin-libdir && mkdir ensembldb.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ensembldb.buildbin-libdir ensembldb_2.11.3.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL ensembldb_2.11.3.zip && rm ensembldb_2.11.3.tar.gz ensembldb_2.11.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1221k  100 1221k    0     0  17.1M      0 --:--:-- --:--:-- --:--:-- 18.9M

install for i386

* installing *source* package 'ensembldb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ensembldb'
    finding HTML links ... done
    Deprecated                              html  
    EnsDb-AnnotationDbi                     html  
    EnsDb-class                             html  
    EnsDb-exonsBy                           html  
    finding level-2 HTML links ... done

    EnsDb-lengths                           html  
    EnsDb-seqlevels                         html  
    EnsDb-sequences                         html  
    EnsDb-utils                             html  
    EnsDb                                   html  
    Filter-classes                          html  
    ProteinFunctionality                    html  
    cdsToTranscript                         html  
    convertFilter                           html  
    genomeToProtein                         html  
    genomeToTranscript                      html  
    global-filters                          html  
    hasProteinData-EnsDb-method             html  
    listEnsDbs                              html  
    makeEnsemblDbPackage                    html  
    proteinToGenome                         html  
    proteinToTranscript                     html  
    runEnsDbApp                             html  
    transcriptToCds                         html  
    transcriptToGenome                      html  
    transcriptToProtein                     html  
    useMySQL-EnsDb-method                   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 'ensembldb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ensembldb' as ensembldb_2.11.3.zip
* DONE (ensembldb)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'ensembldb' successfully unpacked and MD5 sums checked

Tests output

ensembldb.Rcheck/tests_i386/testthat.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 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)
> 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

Attaching package: 'IRanges'

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

    windows

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 C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmp6JR6ck/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 : Tue Apr 14 22:53:58 2020  !=  Tue Apr 14 22:53:49 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 
 174.65   46.64  430.45

ensembldb.Rcheck/tests_x64/testthat.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 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)
> 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

Attaching package: 'IRanges'

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

    windows

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 C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpMTDLvw/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 : Tue Apr 14 22:59:46 2020  !=  Tue Apr 14 22:59:37 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 19 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 146.62   38.75  224.75

Example timings

ensembldb.Rcheck/examples_i386/ensembldb-Ex.timings

nameusersystemelapsed
EnsDb-AnnotationDbi 2.70 0.8316.90
EnsDb-class2.080.162.24
EnsDb-exonsBy 2.75 1.3712.52
EnsDb-lengths0.970.271.24
EnsDb-seqlevels0.050.000.04
EnsDb-sequences0.020.000.02
EnsDb-utils0.230.000.23
EnsDb1.560.171.74
Filter-classes 4.10 3.72561.06
ProteinFunctionality0.140.030.17
cdsToTranscript1.760.202.33
convertFilter0.020.000.02
genomeToProtein1.440.031.47
genomeToTranscript1.110.201.32
global-filters0.090.000.10
hasProteinData-EnsDb-method0.010.000.01
listEnsDbs000
makeEnsemblDbPackage0.910.021.11
proteinToGenome2.220.112.73
proteinToTranscript0.700.060.77
transcriptToCds0.50.00.5
transcriptToGenome1.210.031.23
transcriptToProtein1.980.062.05
useMySQL-EnsDb-method0.020.000.02

ensembldb.Rcheck/examples_x64/ensembldb-Ex.timings

nameusersystemelapsed
EnsDb-AnnotationDbi2.800.583.45
EnsDb-class1.090.151.25
EnsDb-exonsBy2.440.753.18
EnsDb-lengths1.040.271.32
EnsDb-seqlevels0.070.000.06
EnsDb-sequences0.010.000.02
EnsDb-utils0.270.020.28
EnsDb1.110.201.31
Filter-classes2.011.693.70
ProteinFunctionality0.070.000.06
cdsToTranscript1.690.001.69
convertFilter0.010.000.01
genomeToProtein2.020.042.07
genomeToTranscript1.500.191.68
global-filters0.090.020.11
hasProteinData-EnsDb-method0.020.000.02
listEnsDbs000
makeEnsemblDbPackage0.890.030.97
proteinToGenome2.300.092.39
proteinToTranscript0.990.081.07
transcriptToCds0.640.000.64
transcriptToGenome1.170.011.18
transcriptToProtein1.950.072.02
useMySQL-EnsDb-method000