Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 965/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiTC 1.51.0 (landing page) Nicolas Servant
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.51.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiTC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HiTC_1.51.0.tar.gz |
StartedAt: 2024-12-24 01:38:34 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 01:43:33 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 299.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HiTC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiTC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HiTC_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/HiTC.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'HiTC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'HiTC' version '1.51.0' * 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 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 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' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed directionalityIndex 17.58 0.79 22.57 CQC 5.58 0.35 5.92 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/HiTC.Rcheck/00check.log' for details.
HiTC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL HiTC ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'HiTC' ... ** 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 | 5.58 | 0.35 | 5.92 | |
HTCexp-class | 3.25 | 0.15 | 3.40 | |
HTClist-class | 1.42 | 0.11 | 1.53 | |
Nora_5C | 0.24 | 0.02 | 0.25 | |
binningC | 1.23 | 0.01 | 1.27 | |
directionalityIndex | 17.58 | 0.79 | 22.57 | |
discretize | 0 | 0 | 0 | |
export.my5C | 0 | 0 | 0 | |
exportC | 0 | 0 | 0 | |
extractRegion | 0.40 | 0.03 | 0.44 | |
getAnnotatedRestrictionSites | 0 | 0 | 0 | |
getExpectedCounts | 2.27 | 0.25 | 2.53 | |
getPearsonMap | 0.67 | 0.05 | 0.71 | |
getRestrictionFragmentsPerChromosome | 0 | 0 | 0 | |
import.my5C | 0.13 | 0.00 | 0.12 | |
importC | 0 | 0 | 0 | |
intervalsDist | 0.59 | 0.05 | 0.64 | |
mapC | 4.37 | 0.32 | 4.71 | |
normICE | 0 | 0 | 0 | |
normLGF | 0 | 0 | 0 | |
pca.hic | 0.49 | 0.02 | 0.50 | |
removeIntervals | 0.36 | 0.02 | 0.37 | |
setGenomicFeatures | 0 | 0 | 0 | |
setIntervalScale | 1.04 | 0.04 | 1.10 | |