| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:57 -0400 (Fri, 15 Oct 2021).
|
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 67/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationHubData 1.22.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: AnnotationHubData |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AnnotationHubData_1.22.0.tar.gz |
| StartedAt: 2021-10-14 19:33:36 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:48:38 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 901.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AnnotationHubData_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/AnnotationHubData.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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'
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
validationFunctions 62.86 2.77 65.62
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
validationFunctions 69.72 1.6 71.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
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 - 24 test functions, 1 error, 0 failures
ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Connection refused
Test files with failing tests
test_webAccessFunctions.R
test_ftpDirectoryInfo
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
Execution halted
** running tests for arch 'x64' ...
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 - 24 test functions, 1 error, 0 failures
ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Timed out
Test files with failing tests
test_webAccessFunctions.R
test_ftpDirectoryInfo
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: 2 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.
AnnotationHubData.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/AnnotationHubData_1.22.0.tar.gz && rm -rf AnnotationHubData.buildbin-libdir && mkdir AnnotationHubData.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData_1.22.0.zip && rm AnnotationHubData_1.22.0.tar.gz AnnotationHubData_1.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
25 184k 25 47277 0 0 298k 0 --:--:-- --:--:-- --:--:-- 297k
100 184k 100 184k 0 0 796k 0 --:--:-- --:--:-- --:--:-- 797k
install for i386
* 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
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
install for x64
* installing *source* package 'AnnotationHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHubData' as AnnotationHubData_1.22.0.zip
* DONE (AnnotationHubData)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'AnnotationHubData' successfully unpacked and MD5 sums checked
|
AnnotationHubData.Rcheck/tests_i386/AnnotationHubData_unit_tests.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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 [2021-10-14 19:41:57] Preparer Class: ChEAImportPreparer
complete!
INFO [2021-10-14 19:41:58] 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 [2021-10-14 19:42:00] 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 [2021-10-14 19:42:08] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2021-10-14 19:42:14] 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 [2021-10-14 19:42:28] Preparer Class: EnsemblTwoBitPreparer
INFO [2021-10-14 19:42:36] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... ...
downloaded 13 KB
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
..........
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 [2021-10-14 19:42:40] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2021-10-14 19:42:40] 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
Processing 11 files.
complete!
INFO [2021-10-14 19:42:51] Preparer Class: RefNetImportPreparer
complete!
INFO [2021-10-14 19:42:52] 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.
Timing stopped at: 0 0 2.27
Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Connection refused
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 Oct 14 19:44:34 2021
***********************************************
Number of test functions: 24
Number of errors: 1
Number of failures: 0
1 Test Suite :
AnnotationHubData RUnit Tests - 24 test functions, 1 error, 0 failures
ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Connection refused
Test files with failing tests
test_webAccessFunctions.R
test_ftpDirectoryInfo
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
Execution halted
|
AnnotationHubData.Rcheck/tests_x64/AnnotationHubData_unit_tests.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
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: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.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 [2021-10-14 19:45:18] Preparer Class: ChEAImportPreparer
complete!
INFO [2021-10-14 19:45:18] 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 [2021-10-14 19:45:20] 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 [2021-10-14 19:45:28] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2021-10-14 19:45:34] 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 [2021-10-14 19:45:54] Preparer Class: EnsemblTwoBitPreparer
INFO [2021-10-14 19:46:14] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... ...
downloaded 13 KB
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
..........
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 [2021-10-14 19:46:16] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2021-10-14 19:46:17] 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
Processing 11 files.
complete!
INFO [2021-10-14 19:46:26] Preparer Class: RefNetImportPreparer
complete!
INFO [2021-10-14 19:46:26] 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.
Timing stopped at: 0 0 21.32
Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Timed out
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 Oct 14 19:48:26 2021
***********************************************
Number of test functions: 24
Number of errors: 1
Number of failures: 0
1 Test Suite :
AnnotationHubData RUnit Tests - 24 test functions, 1 error, 0 failures
ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ebi.ac.uk port 21: Timed out
Test files with failing tests
test_webAccessFunctions.R
test_ftpDirectoryInfo
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
Execution halted
|
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AnnotationHubData.Rcheck/examples_i386/AnnotationHubData-Ex.timings
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AnnotationHubData.Rcheck/examples_x64/AnnotationHubData-Ex.timings
|