Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:09 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the HiTC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/HiTC.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. |
Package 879/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiTC 1.38.0 (landing page) Nicolas Servant
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: HiTC |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiTC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiTC_1.38.0.tar.gz |
StartedAt: 2022-04-12 14:18:41 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 14:25:25 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 404.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiTC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiTC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiTC_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/HiTC.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiTC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiTC’ version ‘1.38.0’ * 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 ... OK * checking R 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 69.826 0.582 70.666 mapC 6.950 0.358 7.317 CQC 5.447 0.360 5.814 HTCexp-class 4.821 0.233 5.057 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/HiTC.Rcheck/00check.log’ for details.
HiTC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiTC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 | 5.447 | 0.360 | 5.814 | |
HTCexp-class | 4.821 | 0.233 | 5.057 | |
HTClist-class | 3.002 | 0.103 | 3.111 | |
Nora_5C | 0.424 | 0.006 | 0.430 | |
binningC | 2.240 | 0.023 | 2.263 | |
directionalityIndex | 69.826 | 0.582 | 70.666 | |
discretize | 0.000 | 0.001 | 0.000 | |
export.my5C | 0.000 | 0.000 | 0.001 | |
exportC | 0 | 0 | 0 | |
extractRegion | 1.341 | 0.223 | 1.564 | |
getAnnotatedRestrictionSites | 0.000 | 0.001 | 0.001 | |
getExpectedCounts | 1.890 | 0.216 | 2.086 | |
getPearsonMap | 1.101 | 0.193 | 1.294 | |
getRestrictionFragmentsPerChromosome | 0 | 0 | 0 | |
import.my5C | 0.212 | 0.014 | 0.226 | |
importC | 0.000 | 0.001 | 0.000 | |
intervalsDist | 0.647 | 0.023 | 0.670 | |
mapC | 6.950 | 0.358 | 7.317 | |
normICE | 0.000 | 0.001 | 0.001 | |
normLGF | 0 | 0 | 0 | |
pca.hic | 0.913 | 0.017 | 0.932 | |
removeIntervals | 0.495 | 0.012 | 0.507 | |
setGenomicFeatures | 0.000 | 0.000 | 0.001 | |
setIntervalScale | 1.913 | 0.026 | 1.943 | |