Laurent Gatto
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/rpx |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9d84fbe |
| git_last_commit_date: 2021-08-17 03:17:52 -0400 (Tue, 17 Aug 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the rpx package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rpx.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 1627/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rpx 2.0.3 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: rpx |
| Version: 2.0.3 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rpx_2.0.3.tar.gz |
| StartedAt: 2021-10-15 04:50:23 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:54:55 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 271.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rpx.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:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rpx_2.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/rpx.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 'rpx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rpx' version '2.0.3'
* 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 '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' ... ERROR
Running examples in 'rpx-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cache
> ### Title: Package cache
> ### Aliases: cache rpxCache pxCachedProjects
>
> ### ** Examples
>
>
> ## Default rpx cache
> rpxCache()
class: BiocFileCache
bfccache: C:\Users\biocbuild\AppData\Local/R/cache/R/rpx
bfccount: 6
For more information see: bfcinfo() or bfcquery()
>
> ## Set up your own cache by providing a file or a directory to
> ## BiocFileCache::BiocFileCache()
> my_cache <- BiocFileCache::BiocFileCache(tempfile())
> my_cache
class: BiocFileCache
bfccache: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp0eFUnj\fileace86f291445
bfccount: 0
For more information see: bfcinfo() or bfcquery()
> px <- PXDataset("PXD000001", cache = my_cache)
Querying ProteomeXchange for PXD000001.
Warning in file(file, "rt") :
the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
InternetOpenUrl failed: 'A connection with the server could not be established
'
Error in file(file, "rt") : cannot open the connection
Calls: PXDataset -> read.delim -> read.table -> file
Execution halted
** 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: cache
> ### Title: Package cache
> ### Aliases: cache rpxCache pxCachedProjects
>
> ### ** Examples
>
>
> ## Default rpx cache
> rpxCache()
class: BiocFileCache
bfccache: C:\Users\biocbuild\AppData\Local/R/cache/R/rpx
bfccount: 6
For more information see: bfcinfo() or bfcquery()
>
> ## Set up your own cache by providing a file or a directory to
> ## BiocFileCache::BiocFileCache()
> my_cache <- BiocFileCache::BiocFileCache(tempfile())
> my_cache
class: BiocFileCache
bfccache: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpmE0fWL\file1c982dd0157f
bfccount: 0
For more information see: bfcinfo() or bfcquery()
> px <- PXDataset("PXD000001", cache = my_cache)
Querying ProteomeXchange for PXD000001.
Warning in file(file, "rt") :
the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
InternetOpenUrl failed: 'A connection with the server could not be established
'
Error in file(file, "rt") : cannot open the connection
Calls: PXDataset -> read.delim -> read.table -> file
Execution halted
* 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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/rpx.Rcheck/00check.log'
for details.
rpx.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/rpx_2.0.3.tar.gz && rm -rf rpx.buildbin-libdir && mkdir rpx.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rpx.buildbin-libdir rpx_2.0.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL rpx_2.0.3.zip && rm rpx_2.0.3.tar.gz rpx_2.0.3.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 16222 100 16222 0 0 136k 0 --:--:-- --:--:-- --:--:-- 137k
install for i386
* installing *source* package 'rpx' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rpx'
finding HTML links ... done
PXDataset1 html
PXDataset2 html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/rpx.buildbin-libdir/00LOCK-rpx/00new/rpx/help/pxCacheInfo+2CPXdataset-method.html
cache 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_2.0.3.zip
* DONE (rpx)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'rpx' successfully unpacked and MD5 sums checked
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rpx.Rcheck/tests_i386/testthat.Rout
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.
> # 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")
Project PXD000001 with 10 files
[1] 'erwinia_carotovora.fasta' ... [10] 'PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz'
Use 'pxfiles(.)' to see all files.
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 14 ]
>
> proc.time()
user system elapsed
7.51 0.64 9.50
|
rpx.Rcheck/tests_x64/testthat.Rout
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.
> # 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")
Project PXD000001 with 10 files
[1] 'erwinia_carotovora.fasta' ... [10] 'PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz'
Use 'pxfiles(.)' to see all files.
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 14 ]
>
> proc.time()
user system elapsed
7.60 0.32 9.31
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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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