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This page was generated on 2016-10-13 12:52:34 -0700 (Thu, 13 Oct 2016).
Package 957/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
RefNet 1.8.0 Paul Shannon
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | ||||||
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
Package: RefNet |
Version: 1.8.0 |
Command: rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.8.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.8.0.tar.gz |
StartedAt: 2016-10-13 08:02:21 -0700 (Thu, 13 Oct 2016) |
EndedAt: 2016-10-13 08:11:30 -0700 (Thu, 13 Oct 2016) |
EllapsedTime: 548.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RefNet.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.8.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RefNet.Rcheck' * using R version 3.3.1 (2016-06-21) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'RefNet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RefNet' version '1.8.0' * 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 'RefNet' 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. * 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 ** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... OK * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed RefNet-class 24.53 0.76 46.86 interactions 23.03 0.74 25.28 providerClasses 22.62 0.73 24.96 providers 20.31 0.61 22.69 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed RefNet-class 23.88 0.85 27.19 interactions 21.42 0.97 23.89 providerClasses 20.57 0.68 24.43 providers 19.78 0.74 22.35 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' Warning message: running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1 ERROR Running the tests in 'tests/runTests.R' failed. Last 13 lines of output: FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE Test files with failing tests test_RefNet.R test_pubmedAbstract Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet Execution halted ** running tests for arch 'x64' ... Running 'runTests.R' Warning message: running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1 ERROR Running the tests in 'tests/runTests.R' failed. Last 13 lines of output: FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE Test files with failing tests test_RefNet.R test_pubmedAbstract Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet Execution halted * 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: 2 ERRORs, 1 NOTE See 'E:/biocbld/bbs-3.3-bioc/meat/RefNet.Rcheck/00check.log' for details.
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require(RefNet) || stop("unable to load RefNet package") Loading required package: RefNet Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: PSICQUIC Loading required package: biomaRt Loading required package: httr Loading required package: plyr Attaching package: 'plyr' The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename Loading required package: AnnotationHub Loading required package: RCurl Loading required package: bitops Loading required package: shiny [1] TRUE > BiocGenerics:::testPackage('RefNet') Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache The following object is masked from 'package:httr': content [1] initializing PSICQUIC... [1] initializing RefNet from AnnotationHub... snapshotDate(): 2016-10-11 loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769' [1] RefNet ready. checking for biomart access... does 'http://www.ensembl.org' respond? creating ensembl mart hsapiens_gene_ensembl dataset provided? connecting to biomart... [1] "--- test_.combinations" [1] "--- test_.filterOnColumnValue" [1] "--- test_.findHits" [1] "--- test_.smartRbind" [1] "--- test_ctor" [1] initializing PSICQUIC... [1] initializing RefNet from AnnotationHub... snapshotDate(): 2016-10-11 loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769' [1] RefNet ready. [1] "--- test_detectDuplicateInteractions" [1] "--- test_interactions" [1] "--- test_pickBestFromDupGroup" [1] "--- test_providerMix_PSICQUIC_and_native" [1] "--- test_pubmedAbstract" Timing stopped at: 0 0 0.23 Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE In addition: Warning messages: 1: In is.na(psicquic) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(refnet@psicquic) : is.na() applied to non-(list or vector) of type 'S4' 3: In is.na(refnet@psicquic) : is.na() applied to non-(list or vector) of type 'S4' [1] "--- test_recon2Interactions" RUNIT TEST PROTOCOL -- Thu Oct 13 08:11:23 2016 *********************************************** Number of test functions: 11 Number of errors: 0 Number of failures: 1 1 Test Suite : RefNet RUnit Tests - 11 test functions, 0 errors, 1 failure FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE Test files with failing tests test_RefNet.R test_pubmedAbstract Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet Execution halted
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require(RefNet) || stop("unable to load RefNet package") Loading required package: RefNet Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: PSICQUIC Loading required package: biomaRt Loading required package: httr Loading required package: plyr Attaching package: 'plyr' The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename Loading required package: AnnotationHub Loading required package: RCurl Loading required package: bitops Loading required package: shiny [1] TRUE > BiocGenerics:::testPackage('RefNet') Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache The following object is masked from 'package:httr': content [1] initializing PSICQUIC... [1] initializing RefNet from AnnotationHub... snapshotDate(): 2016-10-11 loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769' [1] RefNet ready. checking for biomart access... does 'http://www.ensembl.org' respond? creating ensembl mart hsapiens_gene_ensembl dataset provided? connecting to biomart... [1] "--- test_.combinations" [1] "--- test_.filterOnColumnValue" [1] "--- test_.findHits" [1] "--- test_.smartRbind" [1] "--- test_ctor" [1] initializing PSICQUIC... [1] initializing RefNet from AnnotationHub... snapshotDate(): 2016-10-11 loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768' loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769' [1] RefNet ready. [1] "--- test_detectDuplicateInteractions" [1] "--- test_interactions" [1] "--- test_pickBestFromDupGroup" [1] "--- test_providerMix_PSICQUIC_and_native" [1] "--- test_pubmedAbstract" Timing stopped at: 0 0 0.25 Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE In addition: Warning messages: 1: In is.na(psicquic) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(refnet@psicquic) : is.na() applied to non-(list or vector) of type 'S4' 3: In is.na(refnet@psicquic) : is.na() applied to non-(list or vector) of type 'S4' [1] "--- test_recon2Interactions" RUNIT TEST PROTOCOL -- Thu Oct 13 08:10:15 2016 *********************************************** Number of test functions: 11 Number of errors: 0 Number of failures: 1 1 Test Suite : RefNet RUnit Tests - 11 test functions, 0 errors, 1 failure FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) : Test not TRUE Test files with failing tests test_RefNet.R test_pubmedAbstract Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet Execution halted
RefNet.Rcheck/00install.out:
install for i386 * installing *source* package 'RefNet' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'RefNet' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RefNet' as RefNet_1.8.0.zip * DONE (RefNet)
RefNet.Rcheck/examples_i386/RefNet-Ex.timings:
name | user | system | elapsed | |
RefNet-class | 24.53 | 0.76 | 46.86 | |
detectDuplicateInteractions | 0.01 | 0.00 | 0.02 | |
interactions | 23.03 | 0.74 | 25.28 | |
pickBestFromDupGroup | 0.03 | 0.00 | 0.03 | |
providerClasses | 22.62 | 0.73 | 24.96 | |
providers | 20.31 | 0.61 | 22.69 | |
pubmedAbstract | 0.01 | 0.00 | 0.34 | |
RefNet.Rcheck/examples_x64/RefNet-Ex.timings:
name | user | system | elapsed | |
RefNet-class | 23.88 | 0.85 | 27.19 | |
detectDuplicateInteractions | 0.03 | 0.00 | 0.03 | |
interactions | 21.42 | 0.97 | 23.89 | |
pickBestFromDupGroup | 0.02 | 0.02 | 0.03 | |
providerClasses | 20.57 | 0.68 | 24.43 | |
providers | 19.78 | 0.74 | 22.35 | |
pubmedAbstract | 0.00 | 0.00 | 0.32 | |