| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:22:47 -0400 (Sat, 13 Apr 2019).
| Package 58/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnnotationHub 2.14.5 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 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: AnnotationHub |
| Version: 2.14.5 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AnnotationHub_2.14.5.tar.gz |
| StartedAt: 2019-04-13 00:29:59 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:34:51 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 292.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AnnotationHub.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AnnotationHub_2.14.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/AnnotationHub.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.14.5'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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:
'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 or elapsed time > 5s
user system elapsed
AnnotationHub-class 40.44 1.55 42.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
AnnotationHub-class 37.39 1.44 39.04
* 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-3.8-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.
AnnotationHub.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/AnnotationHub_2.14.5.tar.gz && rm -rf AnnotationHub.buildbin-libdir && mkdir AnnotationHub.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHub.buildbin-libdir AnnotationHub_2.14.5.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL AnnotationHub_2.14.5.zip && rm AnnotationHub_2.14.5.tar.gz AnnotationHub_2.14.5.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
8 199k 8 16384 0 0 425k 0 --:--:-- --:--:-- --:--:-- 457k
100 199k 100 199k 0 0 5162k 0 --:--:-- --:--:-- --:--:-- 5533k
install for i386
* installing *source* package 'AnnotationHub' ...
** 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
getAnnotationHubOption html
listResources html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'AnnotationHub' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHub' as AnnotationHub_2.14.5.zip
* DONE (AnnotationHub)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'AnnotationHub' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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AnnotationHub.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
require("xxx_foo")
RUNIT TEST PROTOCOL -- Sat Apr 13 00:34:23 2019
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHub RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: 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
19.00 1.87 22.92
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AnnotationHub.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
require("xxx_foo")
RUNIT TEST PROTOCOL -- Sat Apr 13 00:34:46 2019
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHub RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: 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
17.82 2.00 22.28
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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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