Tony Chiang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ScISI |
| Branch: RELEASE_3_12 |
| Last Commit: 7fafccc |
| Last Changed Date: 2020-10-27 10:27:58 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:28 -0400 (Thu, 06 May 2021).
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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 1644/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScISI 1.62.0 (landing page) Tony Chiang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ScISI |
| Version: 1.62.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ScISI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ScISI_1.62.0.tar.gz |
| StartedAt: 2021-05-06 06:41:23 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:44:13 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 169.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScISI.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ScISI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ScISI_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ScISI.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ScISI/DESCRIPTION' ... OK * this is package 'ScISI' version '1.62.0' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ScISI.Rcheck/00check.log' for details.
ScISI.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ScISI_1.62.0.tar.gz && rm -rf ScISI.buildbin-libdir && mkdir ScISI.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ScISI.buildbin-libdir ScISI_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ScISI_1.62.0.zip && rm ScISI_1.62.0.tar.gz ScISI_1.62.0.zip
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install for i386
* 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
converting help for package 'ScISI'
finding HTML links ... done
Desc-methods html
ID-methods html
JaccardCoef html
ScISI html
ScISI2html html
arp23 html
arp23G html
arp23Orf html
arp23Y2HG html
calcGraphStats html
cfia html
cfiaOrf html
checkComplex html
checkSGN html
compBijection html
compareComplex html
createGODataFrame html
createGOMatrix html
createMipsDataFrame html
createMipsMatrix html
createYeastDataObj html
dataS html
eAt html
eAt2 html
edgeProp html
egEBI16112 html
expStats html
findSubComp html
gavin2mergeMG html
getAPMSData html
getGOInfo html
getLocOrfs html
getMipsInfo html
getURL-methods html
graphSumStats html
ho2mergeMGG html
krogan2mergeMGGH html
locScISI html
mapping2SysG html
mappingsG html
maximizeSimilarity html
meanDeg html
mergeBGMat html
mips2go html
nAt html
nAtMap html
nonGenes html
nucComp html
recCompSize html
redundantM html
rmByEvi html
runAlignment html
runCompareComplex html
subCompM html
sumStats html
unWantedComp html
unwanted html
xtraGO html
xtraGONodes html
yeastData-class html
** 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
install for x64
* installing *source* package 'ScISI' ...
** 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'
* MD5 sums
packaged installation of 'ScISI' as ScISI_1.62.0.zip
* DONE (ScISI)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ScISI' successfully unpacked and MD5 sums checked
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ScISI.Rcheck/examples_i386/ScISI-Ex.timings
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ScISI.Rcheck/examples_x64/ScISI-Ex.timings
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