Johannes Rainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ensembldb |
| Branch: RELEASE_3_6 |
| Last Commit: d71610e |
| Last Changed Date: 2018-02-14 02:24:35 -0400 (Wed, 14 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:57 -0400 (Thu, 12 Apr 2018).
| Package 424/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ensembldb 2.2.2 Johannes Rainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ensembldb |
| Version: 2.2.2 |
| Command: rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_2.2.2.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_2.2.2.tar.gz |
| StartedAt: 2018-04-11 23:47:22 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:59:46 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 743.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ensembldb.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_2.2.2.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_2.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ensembldb.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '2.2.2'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:55: missing file link 'GeneIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:58: missing file link 'GeneBiotypeFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:61: missing file link 'EntrezFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:64: missing file link 'TxIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:67: missing file link 'TxBiotypeFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:70: missing file link 'ExonIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:73: missing file link 'ExonRankFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:76: missing file link 'SeqNameFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:79: missing file link 'SeqStrandFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:83: missing file link 'GeneStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:84: missing file link 'TxStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:85: missing file link 'ExonStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:89: missing file link 'GeneEndFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:90: missing file link 'TxEndFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:91: missing file link 'ExonEndFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-AnnotationDbi.Rd:75: missing file link 'mapIds'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:156: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:162: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:194: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:243: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:39: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:40: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:44: missing file link 'GeneIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:47: missing file link 'GeneStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:166: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:171: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:252: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:363: missing file link 'GeneIdFilter'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ensembldb.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 3.3Mb
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EnsDb-AnnotationDbi 4.07 0.96 59.37
Filter-classes 2.15 1.78 59.91
EnsDb-exonsBy 1.88 1.03 17.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EnsDb-AnnotationDbi 6.3 1.25 7.55
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/ensembldb.Rcheck/00check.log'
for details.
ensembldb.Rcheck/00install.out
install for i386
* installing *source* package 'ensembldb' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ensembldb'
finding HTML links ... done
Deprecated html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:55: missing file link 'GeneIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:58: missing file link 'GeneBiotypeFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:61: missing file link 'EntrezFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:64: missing file link 'TxIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:67: missing file link 'TxBiotypeFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:70: missing file link 'ExonIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:73: missing file link 'ExonRankFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:76: missing file link 'SeqNameFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:79: missing file link 'SeqStrandFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:83: missing file link 'GeneStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:84: missing file link 'TxStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:85: missing file link 'ExonStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:89: missing file link 'GeneEndFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:90: missing file link 'TxEndFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Deprecated.Rd:91: missing file link 'ExonEndFilter'
EnsDb-AnnotationDbi html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-AnnotationDbi.Rd:75: missing file link 'mapIds'
EnsDb-class html
EnsDb-exonsBy html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:156: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:162: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:194: missing file link 'exonsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/EnsDb-exonsBy.Rd:243: missing file link 'exonsByOverlaps'
EnsDb-lengths html
EnsDb-seqlevels html
EnsDb-sequences html
EnsDb-utils html
EnsDb html
Filter-classes html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:39: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:40: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:44: missing file link 'GeneIdFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:47: missing file link 'GeneStartFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:166: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:171: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:252: missing file link 'GRangesFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkP3zX/R.INSTALL1a543eef4c39/ensembldb/man/Filter-classes.Rd:363: missing file link 'GeneIdFilter'
ProteinFunctionality html
convertFilter html
global-filters html
hasProteinData-EnsDb-method html
listEnsDbs html
makeEnsemblDbPackage html
runEnsDbApp html
useMySQL-EnsDb-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ensembldb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ensembldb' as ensembldb_2.2.2.zip
* DONE (ensembldb)
In R CMD INSTALL
In R CMD INSTALL
|
ensembldb.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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.v75)
> edb <- EnsDb.Hsapiens.v75
>
> test_check("ensembldb")
Creating package in C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\Rtmp6TC27L/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 : Wed Apr 11 23:55:57 2018 != Wed Apr 11 23:55:47 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
Comparing protein data:
protein IDs: (105238) common, (0) only in x, (0) only in y.
Transcript IDs: (105238) identical, (0) different.
Protein sequence: (105238) identical, (0) different.
Done. Result: OK
== testthat results ===========================================================
OK: 1054 SKIPPED: 3 FAILED: 0
There were 18 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
67.92 23.65 157.39
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ensembldb.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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.v75)
> edb <- EnsDb.Hsapiens.v75
>
> test_check("ensembldb")
Creating package in C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpsVAeqs/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 : Wed Apr 11 23:58:21 2018 != Wed Apr 11 23:58:11 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
Comparing protein data:
protein IDs: (105238) common, (0) only in x, (0) only in y.
Transcript IDs: (105238) identical, (0) different.
Protein sequence: (105238) identical, (0) different.
Done. Result: OK
== testthat results ===========================================================
OK: 1054 SKIPPED: 3 FAILED: 0
There were 11 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
81.60 24.32 145.56
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ensembldb.Rcheck/examples_i386/ensembldb-Ex.timings
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ensembldb.Rcheck/examples_x64/ensembldb-Ex.timings
|