Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:35 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 980/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiTC 1.48.0 (landing page) Nicolas Servant
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the HiTC package: - 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: 1.48.0 |
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_1.48.0.tar.gz |
StartedAt: 2024-05-06 22:14:32 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 22:16:16 -0400 (Mon, 06 May 2024) |
EllapsedTime: 104.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HiTC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HiTC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiTC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiTC’ version ‘1.48.0’ * 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 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: consV countMatches glm.nb queryHits Rle 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 ... 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 8.343 0.109 8.461 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/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/4.4-arm64/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 | 1.760 | 0.078 | 1.838 | |
HTCexp-class | 0.723 | 0.038 | 0.761 | |
HTClist-class | 0.684 | 0.015 | 0.700 | |
Nora_5C | 0.065 | 0.002 | 0.068 | |
binningC | 0.310 | 0.005 | 0.315 | |
directionalityIndex | 8.343 | 0.109 | 8.461 | |
discretize | 0 | 0 | 0 | |
export.my5C | 0 | 0 | 0 | |
exportC | 0 | 0 | 0 | |
extractRegion | 0.098 | 0.002 | 0.100 | |
getAnnotatedRestrictionSites | 0 | 0 | 0 | |
getExpectedCounts | 0.373 | 0.089 | 0.454 | |
getPearsonMap | 0.161 | 0.018 | 0.178 | |
getRestrictionFragmentsPerChromosome | 0 | 0 | 0 | |
import.my5C | 0.028 | 0.003 | 0.031 | |
importC | 0 | 0 | 0 | |
intervalsDist | 0.137 | 0.018 | 0.155 | |
mapC | 1.542 | 0.224 | 1.793 | |
normICE | 0 | 0 | 0 | |
normLGF | 0 | 0 | 0 | |
pca.hic | 0.143 | 0.004 | 0.148 | |
removeIntervals | 0.081 | 0.003 | 0.085 | |
setGenomicFeatures | 0 | 0 | 0 | |
setIntervalScale | 0.251 | 0.006 | 0.258 | |