Laurent Gatto
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rpx |
| Branch: master |
| Last Commit: f31590a |
| Last Changed Date: 2019-01-04 13:12:10 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:17:51 -0400 (Tue, 09 Apr 2019).
| Package 1387/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rpx 1.19.1 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: rpx |
| Version: 1.19.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rpx_1.19.1.tar.gz |
| StartedAt: 2019-04-09 05:38:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:40:58 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 148.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rpx.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rpx_1.19.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rpx.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rpx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rpx' version '1.19.1'
* 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 'rpx' 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 ... OK
* 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
PXDataset-class 4.64 0.31 15.53
** running examples for arch 'x64' ... ERROR
Running examples in 'rpx-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PXDataset-class
> ### Title: Class '"PXDataset"'
> ### Aliases: PXDataset-class class:PXDataset PXDataset
> ### pxfiles,PXDataset-method pxfiles pxget,PXDataset-method pxget
> ### pxid,PXDataset-method pxid pxref,PXDataset-method pxref
> ### pxtax,PXDataset-method pxtax pxurl,PXDataset-method pxurl
> ### show,PXDataset-method
> ### Keywords: classes
>
> ### ** Examples
>
> px <- PXDataset("PXD000001")
> px
Object of class "PXDataset"
Error in function (type, msg, asError = TRUE) : Access denied: 500
Calls: <Anonymous> ... strsplit -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError",
"error", "condition")))
}(67L, "Access denied: 500", TRUE)
== testthat results ===========================================================
OK: 11 SKIPPED: 0 FAILED: 2
1. Error: PXD000001 (@test_px.R#4)
2. Error: pxget uses destdir (@test_px.R#37)
Error: testthat unit tests failed
Execution halted
** 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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/rpx.Rcheck/00check.log'
for details.
rpx.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rpx_1.19.1.tar.gz && rm -rf rpx.buildbin-libdir && mkdir rpx.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rpx.buildbin-libdir rpx_1.19.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rpx_1.19.1.zip && rm rpx_1.19.1.tar.gz rpx_1.19.1.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 10600 100 10600 0 0 156k 0 --:--:-- --:--:-- --:--:-- 175k
install for i386
* installing *source* package 'rpx' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rpx'
finding HTML links ... done
PXDataset-class html
pxannounced 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 'rpx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rpx' as rpx_1.19.1.zip
* DONE (rpx)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rpx' successfully unpacked and MD5 sums checked
|
rpx.Rcheck/tests_i386/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(rpx)
>
> test_check("rpx")
Object of class "PXDataset"
-- 1. Error: PXD000001 (@test_px.R#4) -----------------------------------------
Access denied: 500
1: expect_null(show(px1)) at testthat/test_px.R:4
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: show(px1)
5: show(px1)
6: pxfiles(object)
7: strsplit(getURL(ftpdir, dirlistonly = TRUE), "\n")
8: getURL(ftpdir, dirlistonly = TRUE)
9: curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
10: function (type, msg, asError = TRUE)
{
if (!is.character(type)) {
i = match(type, CURLcodeValues)
typeName = if (is.na(i))
character()
else names(CURLcodeValues)[i]
}
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError",
"error", "condition")))
}(67L, "Access denied: 500", TRUE)
-- 2. Error: pxget uses destdir (@test_px.R#37) -------------------------------
Access denied: 500
1: pxget(px, "erwinia_carotovora.fasta", destdir = tmpdir) at testthat/test_px.R:37
2: pxfiles(object)
3: strsplit(getURL(ftpdir, dirlistonly = TRUE), "\n")
4: getURL(ftpdir, dirlistonly = TRUE)
5: curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
6: function (type, msg, asError = TRUE)
{
if (!is.character(type)) {
i = match(type, CURLcodeValues)
typeName = if (is.na(i))
character()
else names(CURLcodeValues)[i]
}
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError",
"error", "condition")))
}(67L, "Access denied: 500", TRUE)
== testthat results ===========================================================
OK: 11 SKIPPED: 0 FAILED: 2
1. Error: PXD000001 (@test_px.R#4)
2. Error: pxget uses destdir (@test_px.R#37)
Error: testthat unit tests failed
Execution halted
|
rpx.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(rpx)
>
> test_check("rpx")
Object of class "PXDataset"
Id: PXD000001 with 12 files
[1] 'F063721.dat' ... [12] 'generated'
Use 'pxfiles(.)' to see all files.
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
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.......... .......... .......... .......... ..........
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.......... .......... .......... .......... ..........
.......... ........
downloaded 1.6 MB
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
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downloaded 1.6 MB
== testthat results ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
5.46 1.03 44.67
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rpx.Rcheck/examples_i386/rpx-Ex.timings
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rpx.Rcheck/examples_x64/rpx-Ex.timings
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