Nicolas Servant
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/HiTC |
| git_branch: devel |
| git_last_commit: 3449887 |
| git_last_commit_date: 2025-04-15 10:13:26 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 976/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiTC 1.53.0 (landing page) Nicolas Servant
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: HiTC |
| Version: 1.53.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTC |
| StartedAt: 2025-06-17 00:09:36 -0000 (Tue, 17 Jun 2025) |
| EndedAt: 2025-06-17 00:11:49 -0000 (Tue, 17 Jun 2025) |
| EllapsedTime: 133.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTC
###
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* 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
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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