Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-28 11:06:02 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for ensembldb on nebbiolo1


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.

raw results

Package 584/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 2.19.7  (landing page)
Johannes Rainer
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/ensembldb
git_branch: master
git_last_commit: a6e2257
git_last_commit_date: 2022-01-12 05:24:49 -0500 (Wed, 12 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: ensembldb
Version: 2.19.7
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ensembldb
StartedAt: 2022-01-27 16:18:05 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 16:19:50 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 105.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ensembldb
###
##############################################################################
##############################################################################


* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* preparing ‘ensembldb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MySQL-backend.Rmd’ using rmarkdown
--- finished re-building ‘MySQL-backend.Rmd’

--- re-building ‘coordinate-mapping-use-cases.Rmd’ using rmarkdown
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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
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: 'ensembldb'

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

    filter

Fetching CDS for 3 proteins ... 3 found
Checking CDS and protein sequence lengths ... 3/3 OK
Loading required package: grid

Attaching package: 'Gviz'

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

    feature

Fetching CDS for 4 proteins ... 4 found
Checking CDS and protein sequence lengths ... 4/4 OK
Warning: Transcript(s) 'ENST00000554623' do/does not encode a protein
Quitting from lines 301-306 (coordinate-mapping-use-cases.Rmd) 
Error: processing vignette 'coordinate-mapping-use-cases.Rmd' failed with diagnostics:
could not find function "subseq"
--- failed re-building ‘coordinate-mapping-use-cases.Rmd’

--- re-building ‘coordinate-mapping.Rmd’ using rmarkdown
Fetching CDS for 1 proteins ... 1 found
Checking CDS and protein sequence lengths ... 1/1 OK
Fetching CDS for 3 proteins ... 2 found
Checking CDS and protein sequence lengths ... 2/2 OK
Fetching CDS for 1 proteins ... 1 found
Checking CDS and protein sequence lengths ... 1/1 OK
Fetching CDS for 3 proteins ... 3 found
Checking CDS and protein sequence lengths ... 1/3 OK
Fetching CDS for 8 proteins ... 8 found
Checking CDS and protein sequence lengths ... 8/8 OK
--- finished re-building ‘coordinate-mapping.Rmd’

--- re-building ‘ensembldb.Rmd’ using rmarkdown

Attaching package: 'magrittr'

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

    not

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

    subtract

Warning in .formatSeqnameByStyleForQuery(x, sn, ifNotFound) :
  Seqnames: Y could not be mapped to  the seqlevels style of the database (Ensembl)!Returning the orginal seqnames for these.
Warning in .formatSeqnameByStyleForQuery(x, sn, ifNotFound) :
  Seqnames: Y could not be mapped to  the seqlevels style of the database (Ensembl)!Returning the orginal seqnames for these.
Warning in getUTRsByTranscript(x = x, what = "five", columns = columns,  :
  No fiveUTR found!
Warning in getUTRsByTranscript(x = x, what = "three", columns = columns,  :
  No threeUTR found!
Warning in .local(x, by, ...) : No cds found!
Note: ordering of the results might not match ordering of keys!
Note: ordering of the results might not match ordering of keys!
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    hubUrl

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

    cache

snapshotDate(): 2022-01-27
Processing genes ... 
 Attribute availability:
  o gene_id ... OK
  o gene_name ... OK
  o entrezid ... Nope
  o gene_biotype ... OK
OK
Processing transcripts ... 
 Attribute availability:
  o transcript_id ... OK
  o gene_id ... OK
  o source ... OK
  o transcript_name ... OK
OK
Processing exons ... OK
Processing chromosomes ... OK
Processing metadata ... OK
Generating index ... OK
  -------------
Verifying validity of the information in the database:
Checking transcripts ... OK
Checking exons ... OK
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘ensembldb.Rmd’

--- re-building ‘proteins.Rmd’ using rmarkdown
--- finished re-building ‘proteins.Rmd’

SUMMARY: processing the following file failed:
  ‘coordinate-mapping-use-cases.Rmd’

Error: Vignette re-building failed.
Execution halted