Laurent Gatto
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ProteomicsAnnotationHubData |
| Branch: RELEASE_3_9 |
| Last Commit: 9af04fd |
| Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:34:00 -0400 (Wed, 16 Oct 2019).
| Package 1267/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ProteomicsAnnotationHubData 1.14.0 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ProteomicsAnnotationHubData |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProteomicsAnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ProteomicsAnnotationHubData_1.14.0.tar.gz |
| StartedAt: 2019-10-16 06:11:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:18:33 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 400.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ProteomicsAnnotationHubData.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProteomicsAnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ProteomicsAnnotationHubData_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ProteomicsAnnotationHubData.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ProteomicsAnnotationHubData/DESCRIPTION' ... OK * this is package 'ProteomicsAnnotationHubData' version '1.14.0' * 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 'ProteomicsAnnotationHubData' 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 ... NOTE Unexported objects imported by ':::' calls: 'AnnotationHubData:::.httrFileInfo' 'GenomeInfoDb:::lookup_tax_id_by_organism' See the note in ?`:::` about the use of this operator. package 'methods' is used but not declared * 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.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 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ProteomicsAnnotationHubData.Rcheck/00check.log' for details.
ProteomicsAnnotationHubData.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ProteomicsAnnotationHubData_1.14.0.tar.gz && rm -rf ProteomicsAnnotationHubData.buildbin-libdir && mkdir ProteomicsAnnotationHubData.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ProteomicsAnnotationHubData_1.14.0.zip && rm ProteomicsAnnotationHubData_1.14.0.tar.gz ProteomicsAnnotationHubData_1.14.0.zip
###
##############################################################################
##############################################################################
% 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 21043 100 21043 0 0 314k 0 --:--:-- --:--:-- --:--:-- 348k
install for i386
* installing *source* package 'ProteomicsAnnotationHubData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ProteomicsAnnotationHubData'
finding HTML links ... done
PAHD-class html
PAHD html
ProteomicsAnnotationHubData html
identicalRemLoc html
makeAnnotationHubMetadata html
readPahdFiles html
writePahdTemplate 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 'ProteomicsAnnotationHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ProteomicsAnnotationHubData' as ProteomicsAnnotationHubData_1.14.0.zip
* DONE (ProteomicsAnnotationHubData)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ProteomicsAnnotationHubData' successfully unpacked and MD5 sums checked
|
ProteomicsAnnotationHubData.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(ProteomicsAnnotationHubData)
Loading required package: AnnotationHub
Loading required package: BiocGenerics
Loading required package: parallel
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, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: AnnotationHubData
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
This is ProteomicsAnnotationHubData version 1.14.0
Read 'ProteomicsAnnotationHubData()' to get started.
Attaching package: 'ProteomicsAnnotationHubData'
The following object is masked from 'package:AnnotationHubData':
makeAnnotationHubMetadata
>
> test_check("ProteomicsAnnotationHubData")
== testthat results ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
18.65 1.62 20.51
|
ProteomicsAnnotationHubData.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(ProteomicsAnnotationHubData)
Loading required package: AnnotationHub
Loading required package: BiocGenerics
Loading required package: parallel
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, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: AnnotationHubData
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
This is ProteomicsAnnotationHubData version 1.14.0
Read 'ProteomicsAnnotationHubData()' to get started.
Attaching package: 'ProteomicsAnnotationHubData'
The following object is masked from 'package:AnnotationHubData':
makeAnnotationHubMetadata
>
> test_check("ProteomicsAnnotationHubData")
== testthat results ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.32 0.95 17.42
|
|
ProteomicsAnnotationHubData.Rcheck/examples_i386/ProteomicsAnnotationHubData-Ex.timings
|
ProteomicsAnnotationHubData.Rcheck/examples_x64/ProteomicsAnnotationHubData-Ex.timings
|