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This page was generated on 2015-11-10 14:47:23 -0800 (Tue, 10 Nov 2015).
Package 299/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
easyRNASeq 2.6.0 Nicolas Delhomme
| 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: easyRNASeq |
Version: 2.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings easyRNASeq_2.6.0.tar.gz |
StartedAt: 2015-11-10 04:24:09 -0800 (Tue, 10 Nov 2015) |
EndedAt: 2015-11-10 04:29:58 -0800 (Tue, 10 Nov 2015) |
EllapsedTime: 348.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: easyRNASeq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings easyRNASeq_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/easyRNASeq.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 ‘easyRNASeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘easyRNASeq’ version ‘2.6.0’ * 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 ‘easyRNASeq’ can be installed ... [26s/27s] 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 There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.convertToUCSC’ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [14s/14s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ [86s/94s] ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: Bam file: ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded. 3: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded. 5: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded. 7: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded. 9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) : You provided an incorrect BAM parameter; 'paired' should be set to 'FALSE'. 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: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.2-bioc/meat/easyRNASeq.Rcheck/00check.log’ for details.
easyRNASeq.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage("easyRNASeq") Loading required package: GenomicRanges 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 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 Warning messages: 1: Getting the organism name is deprecated. Use an AnnotParam object instead and get its datasource. 2: Getting the organism name is deprecated. Use an AnnotParam object instead and get its datasource. Timing stopped at: 0.017 0.002 5.459 Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2 No validation performed at that stage Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and ending tag mismatch: body line 4 and html Premature end of data in tag html line 2 Timing stopped at: 0.012 0.001 1.627 Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : error in evaluating the argument 'table' in selecting a method for function '%in%': 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 RUNIT TEST PROTOCOL -- Tue Nov 10 04:29:52 2015 *********************************************** Number of test functions: 21 Number of errors: 2 Number of failures: 0 1 Test Suite : easyRNASeq RUnit Tests - 21 test functions, 2 errors, 0 failures ERROR in test_getAnnotation_BiomaRt: Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2 ERROR in test_internal_getAnnotation: Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : error in evaluating the argument 'table' in selecting a method for function '%in%': 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_annotations.R test_getAnnotation_BiomaRt test_internal_getAnnotation Error in BiocGenerics:::testPackage("easyRNASeq") : unit tests failed for package easyRNASeq In addition: Warning messages: 1: In FUN(X[[i]], ...) : Bam file: ACACTG.bam is considered unstranded. 2: In FUN(X[[i]], ...) : Bam file: ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded. 3: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded. 5: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded. 7: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded. 9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) : You provided an incorrect BAM parameter; 'paired' should be set to 'FALSE'. Execution halted
easyRNASeq.Rcheck/00install.out:
* installing *source* package ‘easyRNASeq’ ... ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’ Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’ Creating a generic function for ‘print’ from package ‘base’ in package ‘easyRNASeq’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (easyRNASeq)
easyRNASeq.Rcheck/easyRNASeq-Ex.timings:
name | user | system | elapsed | |
DESeq-methods | 0.001 | 0.000 | 0.001 | |
GenomicRanges-methods | 0.709 | 0.016 | 0.725 | |
IRanges-methods | 0.001 | 0.000 | 0.001 | |
Rsamtools-methods | 0.063 | 0.007 | 0.195 | |
ShortRead-methods | 0.002 | 0.000 | 0.002 | |
easyRNASeq-AnnotParam-accessors | 0.003 | 0.000 | 0.004 | |
easyRNASeq-AnnotParam-class | 0.001 | 0.001 | 0.002 | |
easyRNASeq-AnnotParam | 0.002 | 0.000 | 0.002 | |
easyRNASeq-BamFileList | 0.179 | 0.010 | 0.213 | |
easyRNASeq-BamParam-accessors | 0.002 | 0.000 | 0.002 | |
easyRNASeq-BamParam-class | 0.001 | 0.000 | 0.001 | |
easyRNASeq-BamParam | 0.003 | 0.000 | 0.004 | |
easyRNASeq-RnaSeqParam-accessors | 0.006 | 0.000 | 0.006 | |
easyRNASeq-RnaSeqParam-class | 0.001 | 0.000 | 0.002 | |
easyRNASeq-RnaSeqParam | 0.008 | 0.000 | 0.008 | |
easyRNASeq-accessors | 0.004 | 0.001 | 0.004 | |
easyRNASeq-annotation-methods | 0.001 | 0.000 | 0.001 | |
easyRNASeq-class | 0.001 | 0.001 | 0.002 | |
easyRNASeq-correction-methods | 0.001 | 0.000 | 0.002 | |
easyRNASeq-coverage-methods | 0.001 | 0.000 | 0.001 | |
easyRNASeq-easyRNASeq | 0.002 | 0.000 | 0.002 | |
easyRNASeq-island-methods | 0.001 | 0.000 | 0.002 | |
easyRNASeq-package | 0.002 | 0.000 | 0.002 | |
easyRNASeq-simpleRNASeq | 0.001 | 0.000 | 0.002 | |
easyRNASeq-summarization-methods | 0.001 | 0.000 | 0.002 | |
easyRNASeq-synthetic-transcripts | 0.001 | 0.000 | 0.001 | |
edgeR-methods | 0.001 | 0.001 | 0.001 | |
genomeIntervals-methods | 0.000 | 0.000 | 0.001 | |
parallel-methods | 0.000 | 0.000 | 0.001 | |