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This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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

Package 971/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.50.0  (landing page)
Nicolas Servant
Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025)
git_url: https://git.bioconductor.org/packages/HiTC
git_branch: RELEASE_3_20
git_last_commit: ae10a0b
git_last_commit_date: 2024-10-29 09:40:52 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for HiTC on taishan

To the developers/maintainers of the HiTC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiTC.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: HiTC
Version: 1.50.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTC
StartedAt: 2025-03-07 01:54:37 -0000 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 01:56:44 -0000 (Fri, 07 Mar 2025)
EllapsedTime: 127.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTC
###
##############################################################################
##############################################################################


* checking for file ‘HiTC/DESCRIPTION’ ... OK
* preparing ‘HiTC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiC_analysis.Rnw’ using Sweave
Loading required package: HiTC
Loading required package: IRanges
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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    findMatches

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

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: HiCDataHumanIMR90
'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Warning: file stem ‘./HiTC-plot1’ is not portable
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Plotting chr5chr5...
minrange= 2  - maxrange= 569
Plotting chr5chr6...
minrange= 1  - maxrange= 8
Plotting chr5chr7...
minrange= 1  - maxrange= 8
Plotting chr6chr6...
minrange= 3  - maxrange= 593.02
Plotting chr6chr7...
minrange= 1  - maxrange= 8
Plotting chr7chr7...
minrange= 2  - maxrange= 571
Warning: file stem ‘./HiTC-plot2’ is not portable
Plotting chr5chr5...
minrange= 1  - maxrange= 200
Plotting chr5chr6...
minrange= 1  - maxrange= 200
Plotting chr5chr7...
minrange= 1  - maxrange= 119
Plotting chr6chr5...
minrange= 1  - maxrange= 200
Plotting chr6chr6...
minrange= 1  - maxrange= 200
Plotting chr6chr7...
minrange= 1  - maxrange= 81
Plotting chr7chr5...
minrange= 1  - maxrange= 119
Plotting chr7chr6...
minrange= 1  - maxrange= 81
Plotting chr7chr7...
minrange= 1  - maxrange= 200
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’

Error: processing vignette 'HiC_analysis.Rnw' failed with diagnostics:
 chunk 6 (label = resFrag) 
Error in getRestrictionFragmentsPerChromosome(resSite = "AAGCTT", overhangs5 = 1,  : 
  require(genomePack, character.only = TRUE) is not TRUE

--- failed re-building ‘HiC_analysis.Rnw’

--- re-building ‘HiTC.Rnw’ using Sweave
Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Warning: file stem ‘./HiTC-qcc’ is not portable
Get data ...
Generate quality control plots ...
minrange= 1  - maxrange= 741
Warning: file stem ‘./HiTC-bin5C’ is not portable
Bin size 'xgi' =102420 [3x34140]
Bin size 'ygi' =102420 [3x34140]
minrange= 3  - maxrange= 477.2
Lowess fit ...
Standard deviation calculation ...
Delta=8876.395
Calculating stdev ... 
Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable
Lowess fit ...
Standard deviation calculation ...
Delta=8876.395
Calculating stdev ... 
minrange= 0.027  - maxrange= 2.139
Warning: file stem ‘./HiTC-annot5C’ is not portable
Bin size 'xgi' =102087 [3x34029]
Bin size 'ygi' =102087 [3x34029]
Loading required package: rtracklayer
minrange= 0.5  - maxrange= 10
Warning: file stem ‘./HiTC-comp5C’ is not portable
Bin size 'xgi' =102087 [3x34029]
Bin size 'ygi' =102087 [3x34029]
minrange= 0.5  - maxrange= 10
minrange= 0.5  - maxrange= 10
Warning: file stem ‘./HiTC-mapClist’ is not portable
Plotting chr12chr12...
minrange= 1  - maxrange= 100
Plotting chr12chr13...
minrange= 1  - maxrange= 20
Plotting chr12chr14...
minrange= 1  - maxrange= 39
Plotting chr13chr13...
minrange= 1  - maxrange= 100
Plotting chr13chr14...
minrange= 1  - maxrange= 18
Plotting chr14chr14...
minrange= 1  - maxrange= 100
Warning: file stem ‘./HiTC-mapChic’ is not portable
Plotting chr14chr14...
minrange= 1  - maxrange= 100
Warning: file stem ‘./HiTC-mapNormhic’ is not portable
Lowess fit ...
Plotting chr14chr14...
minrange= 0.015  - maxrange= 2.519
Warning: file stem ‘./HiTC-mapCorhic’ is not portable
Plotting chr14chr14...
minrange= 0  - maxrange= 1
Warning: file stem ‘./HiTC-mapPCAhic’ is not portable
Lowess fit ...
--- finished re-building ‘HiTC.Rnw’

SUMMARY: processing the following file failed:
  ‘HiC_analysis.Rnw’

Error: Vignette re-building failed.
Execution halted