Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:05:36 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 MBQN on nebbiolo2


To the developers/maintainers of the MBQN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MBQN.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 1066/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBQN 2.6.0  (landing page)
Ariane Schad
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/MBQN
git_branch: RELEASE_3_14
git_last_commit: 3e5b754
git_last_commit_date: 2021-10-26 12:55:27 -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    OK    ERROR    OK  

Summary

Package: MBQN
Version: 2.6.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MBQN.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MBQN_2.6.0.tar.gz
StartedAt: 2022-01-18 08:11:00 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 08:13:06 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 125.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MBQN.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MBQN.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MBQN_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MBQN.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBQN/DESCRIPTION’ ... OK
* this is package ‘MBQN’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MBQN’ 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
* 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
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rmarkdown’ ‘xml2’
  All declared Imports should be used.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MBQN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPXDfile
> ### Title: Download data from PRIDE
> ### Aliases: getPXDfile
> 
> ### ** Examples
> 
> ## Download protein LFQ intensities of PXD001584 from PRIDE
> getPXDfile(pxd_id = "PXD001584")
Loading PXD001584 from cache.
Project PXD001584 files (20):
 [remote] MaxQuantOutput.tar.gz
 [remote] 20141119_AlCH_1WT_20_2h_n3_1_1200.raw
 [remote] 20141119_AlCH_1WT_20_2h_n3_2_1201.raw
 [remote] 20141119_AlCH_1WT_20_2h_n3_3_1202.raw
 [remote] 20141119_AlCH_3D8_20_2h_n3_1_1206.raw
 [remote] 20141119_AlCH_3D8_20_2h_n3_2_1207.raw
 [remote] 20141119_AlCH_3D8_20_2h_n3_3_1208.raw
 [remote] 20141119_AlCH_1WT_20_2h_n4_1_1212.raw
 [remote] 20141119_AlCH_1WT_20_2h_n4_2_1213.raw
 [remote] 20141119_AlCH_1WT_20_2h_n4_3_1214.raw
 ...
using temporary cache /tmp/RtmpsuYFHP/BiocFileCache
Warning: download failed
  web resource path: ‘ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/01/PXD001584/MaxQuantOutput.tar.gz’
  local file path: ‘/tmp/RtmpsuYFHP/BiocFileCache/262d57a785733_MaxQuantOutput.tar.gz’
  reason: Server denied you to change to the given directory
Warning: bfcadd() failed; resource removed
  rid: BFC1
  fpath: ‘ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/01/PXD001584/MaxQuantOutput.tar.gz’
  reason: download failed
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
Calls: getPXDfile -> <Anonymous> -> <Anonymous> -> .util_download
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MBQN.Rcheck/00check.log’
for details.


Installation output

MBQN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MBQN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘MBQN’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (MBQN)

Tests output


Example timings

MBQN.Rcheck/MBQN-Ex.timings

nameusersystemelapsed
getKminmax0.0010.0000.001