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This page was generated on 2020-04-15 12:42:23 -0400 (Wed, 15 Apr 2020).
| Package 66/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnnotationHubData 1.16.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: AnnotationHubData |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.16.0.tar.gz |
| StartedAt: 2020-04-15 00:23:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:32:24 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 558.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/AnnotationHubData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ... 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
'::' or ':::' import not declared from: ‘stringr’
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
* 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’
.makeComplexGR: no visible binding for global variable ‘seqname’
needToRerunNonStandardOrgDb: no visible binding for global variable
‘results’
needToRerunNonStandardOrgDb: no visible binding for global variable
‘specData’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
variable ‘seqname’
Undefined global functions or variables:
results seqname specData
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
validationFunctions 74.788 1.63 77.049
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘AnnotationHubData_unit_tests.R’
OK
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.
AnnotationHubData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AnnotationHubData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘AnnotationHubData’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHubData)
AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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
INFO [2020-04-15 00:29:42] Preparer Class: ChEAImportPreparer
complete!
INFO [2020-04-15 00:29:42] 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 [2020-04-15 00:29:44] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-84/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-84/gtf/anas_platyrhynchos/
complete!
INFO [2020-04-15 00:30:02] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2020-04-15 00:30:19] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
downloaded 13 KB
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
downloaded 10 KB
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/mCRF/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length 5015 bytes
==================================================
downloaded 5015 bytes
getting file info: E002_RRBS_FractionalMethylation.bigwig
getting file info: E003_RRBS_FractionalMethylation.bigwig
complete!
INFO [2020-04-15 00:30:21] 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 [2020-04-15 00:30:25] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v31.2wayconspseudos.gff3.gz
getting file info: gencode.v31.annotation.gff3.gz
complete!
INFO [2020-04-15 00:30:31] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2020-04-15 00:30:31] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 3818
looking up value for: 90675
looking up value for: 3469
looking up value for: 7957
looking up value for: 4232
Processing 8 files.
complete!
INFO [2020-04-15 00:30:40] Preparer Class: RefNetImportPreparer
complete!
INFO [2020-04-15 00:30:41] Preparer Class: dbSNPVCFPreparer
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_1.0/2016/
complete!
Found invalid DispatchClass.
[1] "somethingNotThere"
For currently available DispatchClass run
'AnnotationHub::DispatchClassList()'
Found invalid DispatchClass.
[1] "somethingNotThere"
For currently available DispatchClass run
'AnnotationHub::DispatchClassList()'
Loading valid species information.
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/
RUNIT TEST PROTOCOL -- Wed Apr 15 00:32:16 2020
***********************************************
Number of test functions: 26
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHubData RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26
Number of errors: 0
Number of failures: 0
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable
>
> proc.time()
user system elapsed
157.706 3.183 204.054
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
| name | user | system | elapsed | |
| AnnotationHubMetadata-class | 0.005 | 0.001 | 0.005 | |
| ImportPreparer-class | 0.001 | 0.001 | 0.002 | |
| makeAnnotationHubMetadata | 0.008 | 0.001 | 0.009 | |
| makeEnsemblFasta | 0.000 | 0.000 | 0.001 | |
| makeGencodeFasta | 0.001 | 0.000 | 0.001 | |
| makeStandardOrgDbs | 0.001 | 0.001 | 0.001 | |
| updateResources | 0.001 | 0.001 | 0.001 | |
| upload_to_S3 | 0 | 0 | 0 | |
| validationFunctions | 74.788 | 1.630 | 77.049 | |