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This page was generated on 2017-03-04 16:50:30 -0500 (Sat, 04 Mar 2017).
| Package 52/1339 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| AnnotationHubData 1.5.25 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | ||||||
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: AnnotationHubData |
| Version: 1.5.25 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.5.25.tar.gz |
| StartedAt: 2017-03-03 23:06:39 -0800 (Fri, 03 Mar 2017) |
| EndedAt: 2017-03-03 23:12:12 -0800 (Fri, 03 Mar 2017) |
| EllapsedTime: 333.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.5.25.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.5.25’
* package encoding: UTF-8
* 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 ‘AnnotationHubData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocInstaller’
A package should be listed in only one of these fields.
* 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' call to ‘BiocInstaller’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
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
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.TxDbPkgMetadataFromObjs: no visible global function definition for
‘dbDisconnect’
.TxDbPkgMetadataFromObjs: no visible global function definition for
‘selectSome’
.makeComplexGR: no visible binding for global variable ‘seqname’
jsonPath: no visible binding for global variable ‘SourceFile’
jsonPath: no visible binding for global variable ‘HubRoot’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Title’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Description’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘BiocVersion’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Genome’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceType’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceUrl’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceVersion’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Species’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘TaxonomyId’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Coordinate_1_based’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘DataProvider’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Maintainer’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataClass’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataDateAdded’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataPath’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘DispatchClass’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Location_Prefix’
test_BioPaxImportPreparer_recipe: no visible binding for global
variable ‘ahroot’
test_BioPaxImportPreparer_recipe: no visible binding for global
variable ‘BiocVersion’
test_BioPaxImportPreparer_recipe: no visible global function definition
for ‘checkTrue’
test_Inparanoid8ImportPreparer_recipe: no visible global function
definition for ‘suppresWarnings’
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
variable ‘ahroot’
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
variable ‘BiocVersion’
test_Inparanoid8ImportPreparer_recipe: no visible global function
definition for ‘checkTrue’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
variable ‘seqname’
Undefined global functions or variables:
BiocVersion Coordinate_1_based DataProvider Description DispatchClass
Genome HubRoot Location_Prefix Maintainer RDataClass RDataDateAdded
RDataPath SourceFile SourceType SourceUrl SourceVersion Species
TaxonomyId Title ahroot checkTrue dbDisconnect results selectSome
seqname specData suppresWarnings
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘AnnotationHubData_unit_tests.R’
ERROR
Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed.
Last 13 lines of output:
1 Test Suite :
AnnotationHubData RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_NCBIImportPreparer_recipe: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Test files with failing tests
test_recipe.R
test_NCBIImportPreparer_recipe
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.
AnnotationHubData_unit_tests.Rout.fail:
R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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("AnnotationHubData")
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
INFO [2017-03-03 23:11:09] Preparer Class: ChEAImportPreparer
complete!
INFO [2017-03-03 23:11:10] Preparer Class: EncodeImportPreparer
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya.broadPeak.gz
complete!
INFO [2017-03-03 23:11:13] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2017-03-03 23:11:21] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2017-03-03 23:11:27] Preparer Class: EpigenomeRoadMapPreparer
getting file info: E002_RRBS_FractionalMethylation.bigwig
getting file info: E003_RRBS_FractionalMethylation.bigwig
complete!
INFO [2017-03-03 23:11:29] Preparer Class: GencodeFastaImportPreparer
getting file info: gencode.v23.chr_patch_hapl_scaff.transcripts.fa.gz
getting file info: gencode.v23.lncRNA_transcripts.fa.gz
complete!
INFO [2017-03-03 23:11:39] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2017-03-03 23:11:47] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2017-03-03 23:11:48] Preparer Class: NCBIImportPreparer
Timing stopped at: 0.007 0.001 0.096
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning messages:
1: In value[[3L]](cond) : chea-background.zip: Service Unavailable
2: In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '', probable reason 'No such file or directory'
INFO [2017-03-03 23:11:49] Preparer Class: PazarImportPreparer
getting file info: pazar_ABS_20120522.csv
getting file info: pazar_AP2g_E2_tan_20120522.csv
getting file info: pazar_AP2g_tan_20120522.csv
getting file info: pazar_AREs_20120522.csv
getting file info: pazar_Atoh1_Klisch_20120522.csv
complete!
INFO [2017-03-03 23:11:50] Preparer Class: RefNetImportPreparer
complete!
INFO [2017-03-03 23:11:52] Preparer Class: dbSNPVCFPreparer
complete!
RUNIT TEST PROTOCOL -- Fri Mar 3 23:12:10 2017
***********************************************
Number of test functions: 21
Number of errors: 1
Number of failures: 0
1 Test Suite :
AnnotationHubData RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_NCBIImportPreparer_recipe: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Test files with failing tests
test_recipe.R
test_NCBIImportPreparer_recipe
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
Execution halted
AnnotationHubData.Rcheck/00install.out:
* installing *source* package ‘AnnotationHubData’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (AnnotationHubData)
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings:
| name | user | system | elapsed | |
| AnnotationHubMetadata-class | 0.005 | 0.000 | 0.005 | |
| ImportPreparer-class | 0.001 | 0.000 | 0.001 | |
| makeAnnotationHubMetadata | 0.001 | 0.001 | 0.001 | |
| makeEnsemblFasta | 0.001 | 0.000 | 0.001 | |
| makeGencodeFasta | 0.001 | 0.000 | 0.001 | |
| readMetadataFromCsv | 0.007 | 0.001 | 0.008 | |
| updateResources | 0.004 | 0.000 | 0.004 | |
| upload_to_S3 | 0.001 | 0.001 | 0.001 | |