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This page was generated on 2022-07-07 11:11:54 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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 Rsamtools on kjohnson


To the developers/maintainers of the Rsamtools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsamtools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1689/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.13.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/Rsamtools
git_branch: master
git_last_commit: 5b8ac23
git_last_commit_date: 2022-05-24 14:43:43 -0400 (Tue, 24 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: Rsamtools
Version: 2.13.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rsamtools
StartedAt: 2022-07-07 03:59:02 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 03:59:53 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 51.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rsamtools
###
##############################################################################
##############################################################################


* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* preparing ‘Rsamtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Rsamtools-Overview.Rnw’ using Sweave
Loading required package: GenomeInfoDb
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: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit


Error: processing vignette 'Rsamtools-Overview.Rnw' failed with diagnostics:
 chunk 17 (label = txdb-transcripts) 
Error in library(TxDb.Hsapiens.UCSC.hg18.knownGene) : 
  there is no package called ‘TxDb.Hsapiens.UCSC.hg18.knownGene’

--- failed re-building ‘Rsamtools-Overview.Rnw’

SUMMARY: processing the following file failed:
  ‘Rsamtools-Overview.Rnw’

Error: Vignette re-building failed.
Execution halted