Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:41 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE ScISI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1597/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ScISI 1.60.0 Tony Chiang
| malbec2 | Linux (Ubuntu 18.04.4 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: ScISI |
Version: 1.60.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ScISI_1.60.0.tar.gz |
StartedAt: 2020-10-17 05:13:33 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 05:15:40 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 126.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ScISI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ScISI_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ScISI.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.60.0’ * 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-3.11-bioc/meat/ScISI.Rcheck/00check.log’ for details.
ScISI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ScISI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘ScISI’ ... ** using staged installation ** 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 from temporary location 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’ ** testing if installed package can be loaded from final location 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’ ** testing if installed package keeps a record of temporary installation path * DONE (ScISI)
ScISI.Rcheck/ScISI-Ex.timings
name | user | system | elapsed | |
JaccardCoef | 0 | 0 | 0 | |
ScISI | 0.031 | 0.004 | 0.034 | |
ScISI2html | 0.000 | 0.000 | 0.001 | |
arp23 | 0.002 | 0.000 | 0.002 | |
arp23G | 0.002 | 0.000 | 0.001 | |
arp23Orf | 0.001 | 0.000 | 0.002 | |
arp23Y2HG | 0.001 | 0.000 | 0.002 | |
cfia | 0.001 | 0.000 | 0.002 | |
cfiaOrf | 0.001 | 0.000 | 0.001 | |
createGODataFrame | 0 | 0 | 0 | |
createGOMatrix | 0.000 | 0.000 | 0.001 | |
createMipsMatrix | 0 | 0 | 0 | |
createYeastDataObj | 0.001 | 0.000 | 0.000 | |
dataS | 0.001 | 0.000 | 0.002 | |
eAt | 0.001 | 0.000 | 0.002 | |
eAt2 | 0.001 | 0.000 | 0.001 | |
egEBI16112 | 0.001 | 0.000 | 0.001 | |
expStats | 0.002 | 0.000 | 0.001 | |
findSubComp | 0 | 0 | 0 | |
gavin2mergeMG | 0.005 | 0.000 | 0.006 | |
getAPMSData | 0.215 | 0.156 | 0.379 | |
getGOInfo | 0.000 | 0.000 | 0.001 | |
getMipsInfo | 0 | 0 | 0 | |
ho2mergeMGG | 0.008 | 0.004 | 0.012 | |
krogan2mergeMGGH | 0.007 | 0.000 | 0.006 | |
locScISI | 0.095 | 0.016 | 0.138 | |
mapping2SysG | 0.000 | 0.002 | 0.003 | |
mappingsG | 0.002 | 0.001 | 0.014 | |
maximizeSimilarity | 0 | 0 | 0 | |
mergeBGMat | 0 | 0 | 0 | |
mips2go | 0.007 | 0.000 | 0.016 | |
nAtMap | 0.000 | 0.002 | 0.002 | |
nonGenes | 0.002 | 0.001 | 0.002 | |
nucComp | 0.003 | 0.000 | 0.003 | |
recCompSize | 0 | 0 | 0 | |
redundantM | 0.002 | 0.000 | 0.002 | |
runAlignment | 0.000 | 0.000 | 0.001 | |
runCompareComplex | 0.001 | 0.000 | 0.000 | |
subCompM | 0.001 | 0.000 | 0.001 | |
sumStats | 0 | 0 | 0 | |
unWantedComp | 0 | 0 | 0 | |
unwanted | 0.001 | 0.000 | 0.001 | |
xtraGO | 0.001 | 0.000 | 0.001 | |
yeastData-class | 0 | 0 | 0 | |