Johannes Rainer
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ensembldb |
| git_branch: RELEASE_3_13 |
| git_last_commit: 130dbcc |
| git_last_commit_date: 2021-08-04 10:18:05 -0400 (Wed, 04 Aug 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ensembldb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ensembldb.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 576/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ensembldb 2.16.4 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ensembldb |
| Version: 2.16.4 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ensembldb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ensembldb_2.16.4.tar.gz |
| StartedAt: 2021-10-14 22:44:52 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:04:29 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 1177.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ensembldb.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ensembldb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ensembldb_2.16.4.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ensembldb.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 'ensembldb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ensembldb' version '2.16.4'
* 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 4.22 4.24 169.69
EnsDb-AnnotationDbi 3.48 0.89 10.43
EnsDb-exonsBy 2.81 1.37 13.07
** 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
ensembldb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ensembldb_2.16.4.tar.gz && rm -rf ensembldb.buildbin-libdir && mkdir ensembldb.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ensembldb.buildbin-libdir ensembldb_2.16.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ensembldb_2.16.4.zip && rm ensembldb_2.16.4.tar.gz ensembldb_2.16.4.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
81 1220k 81 999k 0 0 1474k 0 --:--:-- --:--:-- --:--:-- 1473k
100 1220k 100 1220k 0 0 1615k 0 --:--:-- --:--:-- --:--:-- 1616k
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_2.16.4.zip
* DONE (ensembldb)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ensembldb' successfully unpacked and MD5 sums checked
|
ensembldb.Rcheck/tests_i386/testthat.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.
> 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.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
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: 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\biocbuild\bbs-3.13-bioc\tmpdir\RtmpC0agyX/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 : Thu Oct 14 22:56:21 2021 != Thu Oct 14 22:56:12 2021
- 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
== Skipped tests ===============================================================
* empty test (3)
[ FAIL 0 | WARN 83 | SKIP 3 | PASS 1458 ]
There were 26 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
168.67 48.93 334.06
|
ensembldb.Rcheck/tests_x64/testthat.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.
> 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.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
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: 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\biocbuild\bbs-3.13-bioc\tmpdir\RtmpGmvgAG/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 : Thu Oct 14 23:01:07 2021 != Thu Oct 14 23:00:56 2021
- 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
== Skipped tests ===============================================================
* empty test (3)
[ FAIL 0 | WARN 83 | SKIP 3 | PASS 1458 ]
There were 26 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
175.23 47.67 278.09
|
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ensembldb.Rcheck/examples_i386/ensembldb-Ex.timings
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ensembldb.Rcheck/examples_x64/ensembldb-Ex.timings
|