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This page was generated on 2015-11-10 14:46:28 -0800 (Tue, 10 Nov 2015).
Package 422/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
GenomicFeatures 1.22.4 Bioconductor Package Maintainer
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ ERROR ] | OK | ||||||
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK |
Package: GenomicFeatures |
Version: 1.22.4 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.4.tar.gz |
StartedAt: 2015-11-10 05:13:41 -0800 (Tue, 10 Nov 2015) |
EndedAt: 2015-11-10 05:24:24 -0800 (Tue, 10 Nov 2015) |
EllapsedTime: 643.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicFeatures.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck’ * using R version 3.2.2 Patched (2015-10-08 r69496) * using platform: x86_64-apple-darwin10.8.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.22.4’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘AnnotationDbi’ Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GenomicFeatures’ can be installed ... [21s/22s] 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 * 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 'library' or 'require' calls in package code: ‘FDb.UCSC.tRNAs’ ‘mirbase.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported objects imported by ':::' calls: ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.resort’ ‘AnnotationDbi:::.testForValidKeytype’ ‘AnnotationDbi:::.testSelectArgs’ ‘AnnotationDbi:::.valid.colnames’ ‘AnnotationDbi:::.valid.metadata.table’ ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’ 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 .microRNAs: no visible global function definition for ‘mirbase_dbconn’ supportedMiRBaseBuildValues: no visible global function definition for ‘toTable’ supportedMiRBaseBuildValues: no visible binding for global variable ‘mirbaseSPECIES’ * checking Rd files ... NOTE prepare_Rd: makeTxDbFromGRanges.Rd:43-44: Dropping empty section \details * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenomicFeatures-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeTxDbFromBiomart > ### Title: Make a TxDb object from annotations available on a BioMart > ### database > ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart > ### makeTranscriptDbFromBiomart > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. BASIC USAGE > ## --------------------------------------------------------------------- > > ## We can use listDatasets() from the biomaRt package to list the > ## datasets available in the "ensembl" BioMart database: > library(biomaRt) > head(listDatasets(useMart("ensembl"))) Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and ending tag mismatch: body line 4 and html Premature end of data in tag html line 2 Error in head(listDatasets(useMart("ensembl"))) : error in evaluating the argument 'x' in selecting a method for function 'head': Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2 Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘GenomicFeatures_unit_tests.R’ [156s/166s] ERROR Running the tests in ‘tests/GenomicFeatures_unit_tests.R’ failed. Last 13 lines of output: 6: Premature end of data in tag html line 2 Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures 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: 2 ERRORs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.
GenomicFeatures.Rcheck/tests/GenomicFeatures_unit_tests.Rout.fail:
R version 3.2.2 Patched (2015-10-08 r69496) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (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("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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': anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges 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")'. [1] TRUE > GenomicFeatures:::.test() Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Loading required package: rtracklayer Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and ending tag mismatch: body line 4 and html Premature end of data in tag html line 2 Timing stopped at: 0.007 0 5.155 Error : 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2 Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns RUNIT TEST PROTOCOL -- Tue Nov 10 05:24:14 2015 *********************************************** Number of test functions: 67 Number of errors: 1 Number of failures: 0 1 Test Suite : GenomicFeatures RUnit Tests - 67 test functions, 1 error, 0 failures ERROR in test_makeTxDbFromBiomart: Error : 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2 Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> Execution halted
GenomicFeatures.Rcheck/00install.out:
* installing *source* package ‘GenomicFeatures’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GenomicFeatures)
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:
name | user | system | elapsed | |
DEFAULT_CIRC_SEQS | 0.001 | 0.000 | 0.001 | |
FeatureDb-class | 0.022 | 0.001 | 0.023 | |
TxDb-class | 0.778 | 0.091 | 0.882 | |
as-format-methods | 0.885 | 0.009 | 0.894 | |
coordinate-mapping-methods | 50.586 | 2.998 | 55.798 | |
coverageByTranscript | 57.282 | 13.290 | 70.592 | |
disjointExons | 0.001 | 0.001 | 0.000 | |
extractTranscriptSeqs | 12.374 | 0.181 | 12.623 | |
extractUpstreamSeqs | 2.614 | 0.251 | 3.323 | |
features | 0.061 | 0.002 | 0.063 | |
getPromoterSeq-methods | 1.179 | 0.047 | 1.225 | |
id2name | 0.043 | 0.002 | 0.046 | |
makeFeatureDbFromUCSC | 11.396 | 0.725 | 94.776 | |
makeTxDb | 0.084 | 0.004 | 0.089 | |