| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:55 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the AnnotationHubData package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHubData.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 61/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationHubData 1.25.7 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK |  | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: AnnotationHubData |
| Version: 1.25.7 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AnnotationHubData_1.25.7.tar.gz |
| StartedAt: 2022-03-17 18:26:34 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:34:19 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 464.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AnnotationHubData_1.25.7.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AnnotationHubData.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHubData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHubData' version '1.25.7'
* 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 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 ':::' imports not declared from:
'AzureStor' 'stringr'
'loadNamespace' or 'requireNamespace' call not declared from: 'AzureStor'
Missing objects imported by ':::' calls:
'AnnotationHub:::.db_connection'
'GenomicFeatures:::.makeUCSCChrominfo'
* 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'
oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global
variable 'results'
oldAWSS3_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 (user + system) or elapsed time > 5s
user system elapsed
validationFunctions 60.38 2.72 63.09
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.
AnnotationHubData.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'AnnotationHubData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AnnotationHubData'
finding HTML links ... done
AnnotationHubData-package html
AnnotationHubMetadata-class html
ImportPreparer-class html
flog html
makeAnnotationHubMetadata html
makeEnsemblFasta html
makeGencodeFasta html
makeStandardOrgDbs html
updateResources html
upload_to_S3 html
upload_to_azure html
validationFunctions html
** 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)
Making 'packages.html' ... done
AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: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.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
INFO [2022-03-17 18:31:44] Preparer Class: ChEAImportPreparer
complete!
INFO [2022-03-17 18:31:44] 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 [2022-03-17 18:31:47] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-96/gtf/acanthochromis_polyacanthus/
ftp://ftp.ensembl.org/pub/release-96/gtf/ailuropoda_melanoleuca/
acanthochromis_polyacanthus
acanthochromis_polyacanthus
ailuropoda_melanoleuca
ailuropoda_melanoleuca
acanthochromis_polyacanthus
acanthochromis_polyacanthus
ailuropoda_melanoleuca
ailuropoda_melanoleuca
complete!
INFO [2022-03-17 18:31:55] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2022-03-17 18:32:01] Preparer Class: EnsemblTwoBitPreparer
acanthochromis_polyacanthus
acanthochromis_polyacanthus
acanthochromis_polyacanthus
acanthochromis_polyacanthus
ailuropoda_melanoleuca
acanthochromis_polyacanthus
acanthochromis_polyacanthus
acanthochromis_polyacanthus
acanthochromis_polyacanthus
ailuropoda_melanoleuca
complete!
INFO [2022-03-17 18:32:14] Preparer Class: EnsemblTwoBitPreparer
INFO [2022-03-17 18:32:22] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2022-03-17 18:32:22] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 3818
looking up value for: 106335
looking up value for: 85692
looking up value for: 3635
looking up value for: 90675
AzureStor not installed.
Regenerating all files
Processing 11 files.
complete!
INFO [2022-03-17 18:32:29] Preparer Class: RefNetImportPreparer
complete!
INFO [2022-03-17 18:32:44] 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://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
RUNIT TEST PROTOCOL -- Thu Mar 17 18:34:08 2022
***********************************************
Number of test functions: 23
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHubData RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23
Number of errors: 0
Number of failures: 0
Warning messages:
1: In value[[3L]](cond) :
gerstein-2012.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.
2: In value[[3L]](cond) :
hypoxiaSignaling-2006.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.
3: In value[[3L]](cond) :
stamlabTFs-2012.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.
4: In value[[3L]](cond) :
recon202.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.
>
> proc.time()
user system elapsed
110.15 6.15 185.71
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
| name | user | system | elapsed | |
| AnnotationHubMetadata-class | 0 | 0 | 0 | |
| ImportPreparer-class | 0 | 0 | 0 | |
| makeAnnotationHubMetadata | 0 | 0 | 0 | |
| makeEnsemblFasta | 0 | 0 | 0 | |
| makeGencodeFasta | 0 | 0 | 0 | |
| makeStandardOrgDbs | 0 | 0 | 0 | |
| updateResources | 0 | 0 | 0 | |
| upload_to_S3 | 0 | 0 | 0 | |
| upload_to_azure | 0 | 0 | 0 | |
| validationFunctions | 60.38 | 2.72 | 63.09 | |