Nicolas Servant
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/HiTC |
| git_branch: devel |
| git_last_commit: c174dd2 |
| git_last_commit_date: 2025-10-29 10:10:49 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 983/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiTC 1.55.0 (landing page) Nicolas Servant
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
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. |
| Package: HiTC |
| Version: 1.55.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HiTC_1.55.0.tar.gz |
| StartedAt: 2025-11-01 00:13:25 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 00:19:10 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 344.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HiTC.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HiTC_1.55.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/HiTC.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.55.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HiTC’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
SIGNIFICANT USER-VISIBLE CHANGES
Cannot process chunk/lines:
BUG FIXES
Cannot process chunk/lines:
NEW FEATURES
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 loading without being on the library search path ... 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 ... NOTE
directionalityIndex: no visible global function definition for
‘subjectHits’
directionalityIndex: no visible global function definition for
‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
‘subjectHits’
isBinned,HTCexp: no visible global function definition for
‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
‘subjectHits’
Undefined global functions or variables:
Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* checking Rd files ... WARNING
checkRd: (5) HTClist-class.Rd:52-54: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
import.my5C.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
directionalityIndex 16.609 0.577 17.192
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... WARNING
Warnings in re-building vignettes:
Warning: file stem ‘./HiTC-plot1’ is not portable
Warning: file stem ‘./HiTC-plot2’ is not portable
Warning: file stem ‘./HiTC-normICE’ is not portable
Warning: file stem ‘./HiTC-tads’ is not portable
Warning: file stem ‘./HiTC-di’ is not portable
Warning: file stem ‘./HiTC-qcc’ is not portable
Warning: file stem ‘./HiTC-bin5C’ is not portable
Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable
Warning: file stem ‘./HiTC-annot5C’ is not portable
Warning: file stem ‘./HiTC-comp5C’ is not portable
Warning: file stem ‘./HiTC-mapClist’ is not portable
Warning: file stem ‘./HiTC-mapChic’ is not portable
Warning: file stem ‘./HiTC-mapNormhic’ is not portable
Warning: file stem ‘./HiTC-mapCorhic’ is not portable
Warning: file stem ‘./HiTC-mapPCAhic’ is not portable
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/HiTC.Rcheck/00check.log’
for details.
HiTC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL HiTC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘HiTC’ ... ** this is package ‘HiTC’ version ‘1.55.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HiTC)
HiTC.Rcheck/HiTC-Ex.timings
| name | user | system | elapsed | |
| CQC | 4.826 | 0.105 | 4.932 | |
| HTCexp-class | 2.667 | 0.129 | 2.797 | |
| HTClist-class | 1.129 | 0.015 | 1.146 | |
| Nora_5C | 0.163 | 0.002 | 0.166 | |
| binningC | 0.961 | 0.004 | 0.965 | |
| directionalityIndex | 16.609 | 0.577 | 17.192 | |
| discretize | 0 | 0 | 0 | |
| export.my5C | 0.001 | 0.000 | 0.000 | |
| exportC | 0 | 0 | 0 | |
| extractRegion | 0.267 | 0.008 | 0.275 | |
| getAnnotatedRestrictionSites | 0 | 0 | 0 | |
| getExpectedCounts | 0.995 | 0.318 | 1.218 | |
| getPearsonMap | 0.429 | 0.017 | 0.447 | |
| getRestrictionFragmentsPerChromosome | 0.000 | 0.000 | 0.001 | |
| import.my5C | 0.077 | 0.012 | 0.089 | |
| importC | 0.000 | 0.001 | 0.000 | |
| intervalsDist | 0.324 | 0.007 | 0.331 | |
| mapC | 4.157 | 0.214 | 4.371 | |
| normICE | 0.000 | 0.000 | 0.001 | |
| normLGF | 0.000 | 0.001 | 0.000 | |
| pca.hic | 0.380 | 0.001 | 0.381 | |
| removeIntervals | 0.212 | 0.002 | 0.215 | |
| setGenomicFeatures | 0 | 0 | 0 | |
| setIntervalScale | 0.834 | 0.001 | 0.837 | |