Tony Chiang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ScISI |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1ee59b4 |
| git_last_commit_date: 2021-05-19 11:36:57 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:52 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the ScISI package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ScISI.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1700/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScISI 1.64.0 (landing page) Tony Chiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: ScISI |
| Version: 1.64.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ScISI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ScISI_1.64.0.tar.gz |
| StartedAt: 2021-10-14 23:41:32 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:44:27 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 174.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScISI.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ScISI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ScISI_1.64.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ScISI.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ScISI/DESCRIPTION’ ... OK * this is package ‘ScISI’ version ‘1.64.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ScISI’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘GO.db’ ‘RpsiXML’ ‘annotate’ A package should be listed in only one of these fields. * 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 ... NOTE Package in Depends field not imported from: ‘apComplex’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getGOInfo : <anonymous>: warning in mget(names(parsed[[z]])[these[[z]]], env = org.Sc.sgdGO2ORF, ifnotfound = NA): partial argument match of 'env' to 'envir' getGOInfo: warning in mget(names(cMembers), env = GOCCCHILDREN, ifnotfound = NA): partial argument match of 'env' to 'envir' getGOInfo: warning in mget(names(comp)[alsoThese], env = org.Sc.sgdGO2ORF, ifnotfound = NA): partial argument match of 'env' to 'envir' checkComplex: no visible binding for global variable ‘ScISI’ getAPMSData: no visible binding for global variable ‘yNameTAP’ getAPMSData: no visible binding for global variable ‘MBMEcHMSPCI’ getAPMSData: no visible binding for global variable ‘MBMEcKrogan’ getGOInfo: no visible binding for global variable ‘xtraGO’ getGOInfo: no visible binding for global variable ‘unwanted’ getMipsInfo: no visible binding for global variable ‘nonGenes’ Undefined global functions or variables: MBMEcHMSPCI MBMEcKrogan ScISI nonGenes unwanted xtraGO yNameTAP * checking Rd files ... NOTE prepare_Rd: arp23Orf.Rd:14-15: Dropping empty section \details prepare_Rd: calcGraphStats.Rd:63: Dropping empty section \references prepare_Rd: calcGraphStats.Rd:66-70: Dropping empty section \examples prepare_Rd: checkComplex.Rd:47-48: Dropping empty section \examples prepare_Rd: checkSGN.Rd:24-25: Dropping empty section \note prepare_Rd: checkSGN.Rd:26-28: Dropping empty section \examples prepare_Rd: compBijection.Rd:68-69: Dropping empty section \examples prepare_Rd: compareComplex.Rd:45-47: Dropping empty section \examples prepare_Rd: createMipsDataFrame.Rd:35-37: Dropping empty section \examples prepare_Rd: edgeProp.Rd:25-27: Dropping empty section \details prepare_Rd: edgeProp.Rd:37-39: Dropping empty section \examples prepare_Rd: getLocOrfs.Rd:60-61: Dropping empty section \examples prepare_Rd: graphSumStats.Rd:20-22: Dropping empty section \details prepare_Rd: graphSumStats.Rd:47-49: Dropping empty section \examples prepare_Rd: meanDeg.Rd:21-23: Dropping empty section \details prepare_Rd: meanDeg.Rd:28-29: Dropping empty section \examples prepare_Rd: rmByEvi.Rd:40-42: Dropping empty section \examples prepare_Rd: runCompareComplex.Rd:23-25: Dropping empty section \details prepare_Rd: subCompM.Rd:16-18: Dropping empty section \details prepare_Rd: sumStats.Rd:24-26: Dropping empty section \details prepare_Rd: xtraGONodes.Rd:25-27: Dropping empty section \examples * 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 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ScISI.Rcheck/00check.log’ for details.
ScISI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ScISI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ScISI’ ... ** 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 (ScISI)
ScISI.Rcheck/ScISI-Ex.timings
| name | user | system | elapsed | |
| JaccardCoef | 0.000 | 0.001 | 0.000 | |
| ScISI | 0.054 | 0.009 | 0.063 | |
| ScISI2html | 0.000 | 0.000 | 0.001 | |
| arp23 | 0.001 | 0.001 | 0.004 | |
| arp23G | 0.001 | 0.002 | 0.003 | |
| arp23Orf | 0.001 | 0.002 | 0.003 | |
| arp23Y2HG | 0.002 | 0.003 | 0.004 | |
| cfia | 0.002 | 0.003 | 0.005 | |
| cfiaOrf | 0.002 | 0.003 | 0.005 | |
| createGODataFrame | 0 | 0 | 0 | |
| createGOMatrix | 0.000 | 0.000 | 0.001 | |
| createMipsMatrix | 0.000 | 0.000 | 0.001 | |
| createYeastDataObj | 0 | 0 | 0 | |
| dataS | 0.002 | 0.003 | 0.005 | |
| eAt | 0.002 | 0.002 | 0.003 | |
| eAt2 | 0.001 | 0.003 | 0.004 | |
| egEBI16112 | 0.002 | 0.003 | 0.004 | |
| expStats | 0.001 | 0.003 | 0.004 | |
| findSubComp | 0.001 | 0.001 | 0.001 | |
| gavin2mergeMG | 0.011 | 0.003 | 0.013 | |
| getAPMSData | 0.495 | 0.864 | 1.385 | |
| getGOInfo | 0.000 | 0.001 | 0.000 | |
| getMipsInfo | 0.000 | 0.000 | 0.001 | |
| ho2mergeMGG | 0.012 | 0.003 | 0.015 | |
| krogan2mergeMGGH | 0.008 | 0.002 | 0.011 | |
| locScISI | 0.509 | 0.023 | 0.533 | |
| mapping2SysG | 0.002 | 0.002 | 0.004 | |
| mappingsG | 0.002 | 0.003 | 0.005 | |
| maximizeSimilarity | 0 | 0 | 0 | |
| mergeBGMat | 0.000 | 0.000 | 0.001 | |
| mips2go | 0.006 | 0.002 | 0.008 | |
| nAtMap | 0.001 | 0.002 | 0.003 | |
| nonGenes | 0.001 | 0.002 | 0.003 | |
| nucComp | 0.002 | 0.003 | 0.005 | |
| recCompSize | 0 | 0 | 0 | |
| redundantM | 0.002 | 0.002 | 0.003 | |
| runAlignment | 0.000 | 0.000 | 0.001 | |
| runCompareComplex | 0.001 | 0.000 | 0.000 | |
| subCompM | 0.001 | 0.002 | 0.003 | |
| sumStats | 0 | 0 | 0 | |
| unWantedComp | 0.000 | 0.000 | 0.001 | |
| unwanted | 0.002 | 0.003 | 0.005 | |
| xtraGO | 0.001 | 0.002 | 0.004 | |
| yeastData-class | 0.001 | 0.000 | 0.000 | |