Tony Chiang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ScISI |
| Branch: RELEASE_3_8 |
| Last Commit: c9a6a97 |
| Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:09 -0400 (Tue, 16 Apr 2019).
| Package 1397/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ScISI 1.54.0 Tony Chiang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ScISI |
| Version: 1.54.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ScISI_1.54.0.tar.gz |
| StartedAt: 2019-04-16 02:54:09 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:55:45 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 96.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScISI.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ScISI_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ScISI.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ScISI/DESCRIPTION’ ... OK * this is package ‘ScISI’ version ‘1.54.0’ * 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 ‘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 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.8-bioc/meat/ScISI.Rcheck/00check.log’ for details.
ScISI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ScISI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘ScISI’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’ No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’ No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’ * DONE (ScISI)
ScISI.Rcheck/ScISI-Ex.timings
| name | user | system | elapsed | |
| JaccardCoef | 0 | 0 | 0 | |
| ScISI | 0.028 | 0.008 | 0.037 | |
| ScISI2html | 0 | 0 | 0 | |
| arp23 | 0.004 | 0.000 | 0.002 | |
| arp23G | 0.000 | 0.000 | 0.002 | |
| arp23Orf | 0.004 | 0.000 | 0.002 | |
| arp23Y2HG | 0.000 | 0.000 | 0.002 | |
| cfia | 0.004 | 0.000 | 0.003 | |
| cfiaOrf | 0.000 | 0.000 | 0.002 | |
| createGODataFrame | 0 | 0 | 0 | |
| createGOMatrix | 0 | 0 | 0 | |
| createMipsMatrix | 0 | 0 | 0 | |
| createYeastDataObj | 0.000 | 0.000 | 0.001 | |
| dataS | 0.000 | 0.000 | 0.001 | |
| eAt | 0.000 | 0.000 | 0.002 | |
| eAt2 | 0.004 | 0.000 | 0.002 | |
| egEBI16112 | 0.000 | 0.000 | 0.001 | |
| expStats | 0.024 | 0.004 | 0.027 | |
| findSubComp | 0.004 | 0.000 | 0.001 | |
| gavin2mergeMG | 0.008 | 0.000 | 0.010 | |
| getAPMSData | 0.240 | 0.172 | 0.493 | |
| getGOInfo | 0 | 0 | 0 | |
| getMipsInfo | 0 | 0 | 0 | |
| ho2mergeMGG | 0.008 | 0.000 | 0.007 | |
| krogan2mergeMGGH | 0.008 | 0.000 | 0.005 | |
| locScISI | 0.080 | 0.024 | 0.105 | |
| mapping2SysG | 0.000 | 0.000 | 0.003 | |
| mappingsG | 0.004 | 0.000 | 0.002 | |
| maximizeSimilarity | 0.000 | 0.000 | 0.001 | |
| mergeBGMat | 0 | 0 | 0 | |
| mips2go | 0.000 | 0.004 | 0.006 | |
| nAtMap | 0.000 | 0.000 | 0.002 | |
| nonGenes | 0.000 | 0.000 | 0.003 | |
| nucComp | 0.004 | 0.000 | 0.002 | |
| recCompSize | 0 | 0 | 0 | |
| redundantM | 0.000 | 0.000 | 0.002 | |
| runAlignment | 0 | 0 | 0 | |
| runCompareComplex | 0.000 | 0.000 | 0.001 | |
| subCompM | 0.004 | 0.000 | 0.002 | |
| sumStats | 0 | 0 | 0 | |
| unWantedComp | 0 | 0 | 0 | |
| unwanted | 0.000 | 0.000 | 0.003 | |
| xtraGO | 0.004 | 0.000 | 0.002 | |
| yeastData-class | 0.000 | 0.000 | 0.001 | |