| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:29:54 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the AnnotationHub package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 66/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationHub 2.22.1 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: AnnotationHub |
| Version: 2.22.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationHub_2.22.1.tar.gz |
| StartedAt: 2021-05-06 00:25:35 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:32:56 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 441.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AnnotationHub.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationHub_2.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationHub.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHub/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHub' version '2.22.1'
* 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 'AnnotationHub' 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: 'ensembldb'
Unexported objects imported by ':::' calls:
'BiocFileCache:::.get_tbl_rid' 'BiocManager:::.version_bioc'
'BiocManager:::isDevel'
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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnotationHub-class 51.84 1.2 55.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnotationHub-class 53.23 1.54 56.7
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.
AnnotationHub.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/AnnotationHub_2.22.1.tar.gz && rm -rf AnnotationHub.buildbin-libdir && mkdir AnnotationHub.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHub.buildbin-libdir AnnotationHub_2.22.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AnnotationHub_2.22.1.zip && rm AnnotationHub_2.22.1.tar.gz AnnotationHub_2.22.1.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
100 214k 100 214k 0 0 5018k 0 --:--:-- --:--:-- --:--:-- 5102k
install for i386
* installing *source* package 'AnnotationHub' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AnnotationHub'
finding HTML links ... done
AnnotationHub-class html
AnnotationHub-package html
AnnotationHubResource-class html
Hub-utils html
convertHub html
getAnnotationHubOption html
listResources html
utils 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 'AnnotationHub' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHub' as AnnotationHub_2.22.1.zip
* DONE (AnnotationHub)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AnnotationHub' successfully unpacked and MD5 sums checked
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AnnotationHub.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("AnnotationHub")
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
snapshotDate(): 2020-10-27
snapshotDate(): 2021-05-04
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
require("xxx_foo")
RUNIT TEST PROTOCOL -- Thu May 06 00:31:18 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: download failed
hub path: 'bogus/url'
cache resource: 'AHInvalid : 5012'
reason: all(rtype == "web" | file.exists(fpath)) is not TRUE
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'xxx_foo'
>
> proc.time()
user system elapsed
68.50 6.48 86.93
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AnnotationHub.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("AnnotationHub")
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
snapshotDate(): 2020-10-27
snapshotDate(): 2021-05-04
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
snapshotDate(): 2020-10-27
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
require("xxx_foo")
RUNIT TEST PROTOCOL -- Thu May 06 00:32:52 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: download failed
hub path: 'bogus/url'
cache resource: 'AHInvalid : 5012'
reason: all(rtype == "web" | file.exists(fpath)) is not TRUE
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'xxx_foo'
>
> proc.time()
user system elapsed
80.92 7.29 93.57
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AnnotationHub.Rcheck/examples_i386/AnnotationHub-Ex.timings
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AnnotationHub.Rcheck/examples_x64/AnnotationHub-Ex.timings
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