| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:25 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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To the developers/maintainers of the AnnotationHubData package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 71/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationHubData 1.31.0 (landing page) Bioconductor Package Maintainer
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: AnnotationHubData |
| Version: 1.31.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings AnnotationHubData_1.31.0.tar.gz |
| StartedAt: 2023-06-05 17:11:38 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 17:26:17 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 878.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings AnnotationHubData_1.31.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AnnotationHubData.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.31.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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’
Unexported objects imported by ':::' calls:
‘BiocCheck:::getParent’ ‘GenomeInfoDb:::check_tax_id’
‘GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP’
‘GenomeInfoDb:::lookup_organism_by_tax_id’
‘GenomeInfoDb:::lookup_tax_id_by_organism’
‘GenomicFeatures:::lookup_organism_by_UCSC_genome’
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’
.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 84.654 1.725 86.521
* 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 ...
‘IntroductionToAnnotationHubData.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.
AnnotationHubData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL AnnotationHubData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘AnnotationHubData’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’ ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHubData)
AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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("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, aperm, 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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
INFO [2023-06-05 17:20:05] Preparer Class: ChEAImportPreparer
complete!
INFO [2023-06-05 17:20:07] 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 [2023-06-05 17:20:11] 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 [2023-06-05 17:20:38] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2023-06-05 17:21:00] 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 [2023-06-05 17:23:02] Preparer Class: EnsemblTwoBitPreparer
INFO [2023-06-05 17:23:44] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2023-06-05 17:23:44] Preparer Class: NCBIImportPreparer
looking up value for: 4565
looking up value for: 3708
looking up value for: 3818
looking up value for: 106335
looking up value for: 274614
looking up value for: 85692
AzureStor not installed.
Regenerating all files
Processing 11 files.
complete!
INFO [2023-06-05 17:23:56] Preparer Class: RefNetImportPreparer
complete!
INFO [2023-06-05 17:24:01] 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 -- Mon Jun 5 17:26:12 2023
***********************************************
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 message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'AnnotationForge'
>
> proc.time()
user system elapsed
142.212 10.120 421.718
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
| name | user | system | elapsed | |
| AnnotationHubMetadata-class | 0.002 | 0.000 | 0.002 | |
| ImportPreparer-class | 0 | 0 | 0 | |
| makeAnnotationHubMetadata | 0.004 | 0.000 | 0.004 | |
| 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 | 84.654 | 1.725 | 86.521 | |