Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-24 13:07:08 -0500 (Fri, 24 Dec 2021).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4326
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4075
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4136
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rpx on tokay2


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.

raw results

Package 1652/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rpx 2.2.0  (landing page)
Laurent Gatto
Snapshot Date: 2021-12-23 01:55:07 -0500 (Thu, 23 Dec 2021)
git_url: https://git.bioconductor.org/packages/rpx
git_branch: RELEASE_3_14
git_last_commit: e4d83a3
git_last_commit_date: 2021-10-26 12:12:24 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: rpx
Version: 2.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rpx_2.2.0.tar.gz
StartedAt: 2021-12-24 01:24:11 -0500 (Fri, 24 Dec 2021)
EndedAt: 2021-12-24 01:26:27 -0500 (Fri, 24 Dec 2021)
EllapsedTime: 135.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: rpx.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rpx.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rpx_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/rpx.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.2.0'
* 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-3.14-bioc\tmpdir\Rtmpgr4Vdo\filee8bc732c1b5
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: 'The connection with the server was reset
'
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-3.14-bioc\tmpdir\RtmpqYQ8QH\file119b460cb20d
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: 'The connection with the server was reset
'
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-3.14-bioc/meat/rpx.Rcheck/00check.log'
for details.


Installation output

rpx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/rpx_2.2.0.tar.gz && rm -rf rpx.buildbin-libdir && mkdir rpx.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rpx.buildbin-libdir rpx_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL rpx_2.2.0.zip && rm rpx_2.2.0.tar.gz rpx_2.2.0.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 18151  100 18151    0     0  46163      0 --:--:-- --:--:-- --:--:-- 46303

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-3.14-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_2.2.0.zip
* DONE (rpx)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'rpx' successfully unpacked and MD5 sums checked

Tests output

rpx.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
   7.87    0.48    9.98 

rpx.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
   7.45    0.32    9.09 

Example timings

rpx.Rcheck/examples_i386/rpx-Ex.timings

nameusersystemelapsed
PXDataset14.160.254.74
PXDataset21.920.132.05

rpx.Rcheck/examples_x64/rpx-Ex.timings

nameusersystemelapsed
PXDataset13.440.183.61
PXDataset21.440.211.65