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This page was generated on 2016-04-23 10:18:29 -0700 (Sat, 23 Apr 2016).
Package 531/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
InSilico DB
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
Package: inSilicoMerging |
Version: 1.14.1 |
Command: rm -rf inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && mkdir inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoMerging.buildbin-libdir inSilicoMerging_1.14.1.tar.gz >inSilicoMerging.Rcheck\00install.out 2>&1 && cp inSilicoMerging.Rcheck\00install.out inSilicoMerging-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=inSilicoMerging.buildbin-libdir --install="check:inSilicoMerging-install.out" --force-multiarch --no-vignettes --timings inSilicoMerging_1.14.1.tar.gz |
StartedAt: 2016-04-23 03:49:25 -0700 (Sat, 23 Apr 2016) |
EndedAt: 2016-04-23 03:50:44 -0700 (Sat, 23 Apr 2016) |
EllapsedTime: 79.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: inSilicoMerging.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && mkdir inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoMerging.buildbin-libdir inSilicoMerging_1.14.1.tar.gz >inSilicoMerging.Rcheck\00install.out 2>&1 && cp inSilicoMerging.Rcheck\00install.out inSilicoMerging-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=inSilicoMerging.buildbin-libdir --install="check:inSilicoMerging-install.out" --force-multiarch --no-vignettes --timings inSilicoMerging_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbld/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck' * using R version 3.2.4 (2016-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'inSilicoMerging/DESCRIPTION' ... OK * this is package 'inSilicoMerging' version '1.14.1' * 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 'inSilicoMerging' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... NOTE Package in Depends field not imported from: 'Biobase' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE commonGenes : <anonymous>: no visible global function definition for 'exprs' geneBMCESet: no visible global function definition for 'exprs<-' geneBMCESet: no visible global function definition for 'exprs' geneNormESet: no visible global function definition for 'exprs<-' geneNormESet: no visible global function definition for 'exprs' identify_common_genes: no visible global function definition for 'exprs' makeColorMap: no visible global function definition for 'pData' makeColorVec: no visible global function definition for 'pData' matchExprsPheno: no visible global function definition for 'exprs' matchExprsPheno: no visible global function definition for 'pData<-' matchExprsPheno: no visible global function definition for 'pData' mergeCOMBAT: no visible global function definition for 'pData' mergeCOMBAT: no visible global function definition for 'exprs' mergeCOMBAT: no visible global function definition for 'exprs<-' mergeNONE: no visible global function definition for 'annotation' mergeNONE: no visible global function definition for 'exprs' mergeNONE: no visible global function definition for 'exprs<-' mergeNONE: no visible global function definition for 'pData<-' mergeNONE: no visible global function definition for 'fData<-' mergeNONE: no visible global function definition for 'annotation<-' plotGeneWiseBoxPlot: no visible global function definition for 'exprs' plotGeneWiseBoxPlot: no visible global function definition for 'pData' plotMDS: no visible global function definition for 'exprs' plotMDS: no visible global function definition for 'pData' plotRLE: no visible global function definition for 'exprs' plotRLE: no visible global function definition for 'rowMedians' xpn: no visible global function definition for 'exprs' xpn: no visible global function definition for 'exprs<-' * 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' ... ERROR Running examples in 'inSilicoMerging-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: merge > ### Title: General method to merge different ExpressionSets > ### Aliases: merge > > ### ** Examples > > > # retrieve two datasets: > library(inSilicoDb); Loading required package: rjson Loading required package: RCurl Loading required package: bitops > InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a"); INSILICODB: Welcome RPackage Tester [1] 5296 > eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="GENE"); INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience. Error: Stopped because of previous errors Execution halted ** running examples for arch 'x64' ... ERROR Running examples in 'inSilicoMerging-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: merge > ### Title: General method to merge different ExpressionSets > ### Aliases: merge > > ### ** Examples > > > # retrieve two datasets: > library(inSilicoDb); Loading required package: rjson Loading required package: RCurl Loading required package: bitops > InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a"); INSILICODB: Welcome RPackage Tester [1] 5296 > eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="GENE"); INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience. Error: Stopped because of previous errors Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'inSilicoMerging_unit_tests.R' [6s] Warning message: running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "inSilicoMerging_unit_tests.R" "inSilicoMerging_unit_tests.Rout"' had status 1 ERROR Running the tests in 'tests/inSilicoMerging_unit_tests.R' failed. Last 13 lines of output: inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors Test files with failing tests test_inSilicoMerging.R test.compare_null_bmc_merge Error in BiocGenerics:::testPackage("inSilicoMerging") : unit tests failed for package inSilicoMerging Calls: <Anonymous> -> <Anonymous> Execution halted ** running tests for arch 'x64' ... Running 'inSilicoMerging_unit_tests.R' [6s] Warning message: running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "inSilicoMerging_unit_tests.R" "inSilicoMerging_unit_tests.Rout"' had status 1 ERROR Running the tests in 'tests/inSilicoMerging_unit_tests.R' failed. Last 13 lines of output: inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors Test files with failing tests test_inSilicoMerging.R test.compare_null_bmc_merge Error in BiocGenerics:::testPackage("inSilicoMerging") : unit tests failed for package inSilicoMerging Calls: <Anonymous> -> <Anonymous> 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: 4 ERRORs, 2 NOTEs See 'D:/biocbld/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck/00check.log' for details.
inSilicoMerging_unit_tests.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes" 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("inSilicoMerging") || stop("unable to load inSilicoMerging package") Loading required package: inSilicoMerging Loading required package: Biobase 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, as.vector, 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, unlist, unsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'inSilicoMerging' The following object is masked from 'package:base': merge [1] TRUE > inSilicoMerging:::.test() Loading required package: rjson Loading required package: RCurl Loading required package: bitops INSILICODB: Welcome RPackage Tester INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience. Timing stopped at: 0.47 0.01 3.87 Error : Stopped because of previous errors RUNIT TEST PROTOCOL -- Sat Apr 23 03:50:31 2016 *********************************************** Number of test functions: 1 Number of errors: 1 Number of failures: 0 1 Test Suite : inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors Test files with failing tests test_inSilicoMerging.R test.compare_null_bmc_merge Error in BiocGenerics:::testPackage("inSilicoMerging") : unit tests failed for package inSilicoMerging Calls: <Anonymous> -> <Anonymous> Execution halted
inSilicoMerging_unit_tests.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes" 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("inSilicoMerging") || stop("unable to load inSilicoMerging package") Loading required package: inSilicoMerging Loading required package: Biobase 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, as.vector, 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, unlist, unsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'inSilicoMerging' The following object is masked from 'package:base': merge [1] TRUE > inSilicoMerging:::.test() Loading required package: rjson Loading required package: RCurl Loading required package: bitops INSILICODB: Welcome RPackage Tester INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience. Timing stopped at: 0.45 0.03 3.82 Error : Stopped because of previous errors RUNIT TEST PROTOCOL -- Sat Apr 23 03:50:37 2016 *********************************************** Number of test functions: 1 Number of errors: 1 Number of failures: 0 1 Test Suite : inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors Test files with failing tests test_inSilicoMerging.R test.compare_null_bmc_merge Error in BiocGenerics:::testPackage("inSilicoMerging") : unit tests failed for package inSilicoMerging Calls: <Anonymous> -> <Anonymous> Execution halted
inSilicoMerging.Rcheck/00install.out:
install for i386 * installing *source* package 'inSilicoMerging' ... ** 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 'inSilicoMerging' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'inSilicoMerging' as inSilicoMerging_1.14.1.zip * DONE (inSilicoMerging)
inSilicoMerging.Rcheck/examples_i386/inSilicoMerging-Ex.timings:
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inSilicoMerging.Rcheck/examples_x64/inSilicoMerging-Ex.timings:
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