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This page was generated on 2015-10-27 12:12:13 -0400 (Tue, 27 Oct 2015).
| Package 735/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| OrganismDbi 1.13.0 Biocore Data Team
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK |
| Package: OrganismDbi |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.13.0.tar.gz |
| StartedAt: 2015-10-27 06:31:04 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:39:33 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 509.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OrganismDbi.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.13.0’
* 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 ‘OrganismDbi’ can be installed ... [15s/15s] 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 ... WARNING
'library' or 'require' call not declared from: ‘AnnotationHub’
'library' or 'require' call to ‘GenomicFeatures’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' call to ‘AnnotationHub’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘GenomicFeatures:::.set.group.names’
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.chooseCentralOrgPkgSymbol’
‘AnnotationDbi:::.mapIds’ ‘AnnotationDbi:::.resort’
‘AnnotationDbi:::.testForValidKeytype’
‘AnnotationDbi:::.testSelectArgs’ ‘BiocGenerics:::testPackage’
‘GenomicFeatures:::.makePackageName’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.selectByRanges: no visible global function definition for
‘findOverlaps’
.selectByRanges: no visible global function definition for ‘queryHits’
.selectByRanges: no visible global function definition for
‘subjectHits’
.taxIdToOrgDb: no visible global function definition for
‘AnnotationHub’
.taxIdToOrgDbName: no visible global function definition for
‘AnnotationHub’
available.GTFsForTxDbs: no visible global function definition for
‘AnnotationHub’
makeHubGTFIntoTxDb: no visible global function definition for
‘makeTxDbFromGRanges’
makeOrganismDbFromBiomart: no visible binding for global variable
‘DEFAULT_CIRC_SEQS’
makeOrganismDbFromBiomart: no visible global function definition for
‘makeTxDbFromBiomart’
makeOrganismDbFromTxDb: no visible global function definition for
‘isSingleStringOrNA’
makeOrganismDbFromUCSC: no visible binding for global variable
‘DEFAULT_CIRC_SEQS’
makeOrganismDbFromUCSC: no visible global function definition for
‘makeTxDbFromUCSC’
makeOuterMcolFromInnerMcol: no visible global function definition for
‘elementLengths’
Undefined global functions or variables:
AnnotationHub DEFAULT_CIRC_SEQS elementLengths findOverlaps
isSingleStringOrNA makeTxDbFromBiomart makeTxDbFromGRanges
makeTxDbFromUCSC queryHits subjectHits
* 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 ... WARNING
'library' or 'require' calls not declared from:
‘biomaRt’ ‘rtracklayer’
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/170s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 17.875 0.284 36.218
OrganismDb 8.540 0.060 8.605
rangeBasedAccessors 7.727 0.004 7.737
makeOrganismDbFromTxDb 6.974 0.092 57.598
makeOrganismDbFromUCSC 6.716 0.045 52.380
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘OrganismDbi_unit_tests.R’ [205s/206s]
ERROR
Running the tests in ‘tests/OrganismDbi_unit_tests.R’ failed.
Last 13 lines of output:
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
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, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.
OrganismDbi.Rcheck/tests/OrganismDbi_unit_tests.Rout.fail:
R Under development (unstable) (2015-09-09 r69333) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("OrganismDbi")
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: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Homo.sapiens
Loading required package: GO.db
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db
Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
'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: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 1:1 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 1:1 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 many: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 many:1 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 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Timing stopped at: 1.751 0 1.751
Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
In addition: Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
Loading required package: mirbase.db
Loading required package: FDb.UCSC.tRNAs
RUNIT TEST PROTOCOL -- Tue Oct 27 06:39:31 2015
***********************************************
Number of test functions: 42
Number of errors: 1
Number of failures: 0
1 Test Suite :
OrganismDbi RUnit Tests - 42 test functions, 1 error, 0 failures
ERROR in test_extractTranscriptSeqs: Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
Execution halted
OrganismDbi.Rcheck/00install.out:
* installing *source* package ‘OrganismDbi’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (OrganismDbi)
OrganismDbi.Rcheck/OrganismDbi-Ex.timings:
| name | user | system | elapsed | |
| OrganismDb | 8.540 | 0.060 | 8.605 | |
| coordinate-mapping-method | 0.958 | 0.012 | 0.970 | |
| makeOrganismDbFromBiomart | 17.875 | 0.284 | 36.218 | |
| makeOrganismDbFromTxDb | 6.974 | 0.092 | 57.598 | |
| makeOrganismDbFromUCSC | 6.716 | 0.045 | 52.380 | |
| makeOrganismPackage | 0.002 | 0.000 | 0.002 | |
| rangeBasedAccessors | 7.727 | 0.004 | 7.737 | |