Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:06:52 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MBQN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MBQN_2.6.0.tar.gz
StartedAt: 2022-01-18 22:05:07 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 22:08:24 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 196.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MBQN.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MBQN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MBQN_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MBQN.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 '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 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
* 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
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 ...
** running examples for arch 'i386' ... 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 C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpkdevVq/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: 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpkdevVq/BiocFileCache/89c373a5a50_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
** running examples for arch 'x64' ... 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 C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQXf4Sx/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: 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQXf4Sx/BiocFileCache/2d7c5b165a70_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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MBQN.Rcheck/00check.log'
for details.


Installation output

MBQN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MBQN_2.6.0.tar.gz && rm -rf MBQN.buildbin-libdir && mkdir MBQN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MBQN.buildbin-libdir MBQN_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MBQN_2.6.0.zip && rm MBQN_2.6.0.tar.gz MBQN_2.6.0.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 44629  100 44629    0     0   406k      0 --:--:-- --:--:-- --:--:--  411k

install for i386

* installing *source* package 'MBQN' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MBQN'
    finding HTML links ... done
    example_NApattern                       html  
    getKminmax                              html  
    getPXDfile                              html  
    getPvalue                               html  
    mbqn                                    html  
    mbqnBoxplot                             html  
    mbqnGetIntersect                        html  
    mbqnGetNRIfeatures                      html  
    mbqnGetThreshold                        html  
    mbqnLoadFile                            html  
    mbqnNRI                                 html  
    mbqnPlotAll                             html  
    mbqnPlotRI                              html  
    mbqnSimuData                            html  
    mbqnSimuDistortion                      html  
    oneSidedTest                            html  
    truncateDecimals                        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 'MBQN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MBQN' as MBQN_2.6.0.zip
* DONE (MBQN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MBQN' successfully unpacked and MD5 sums checked

Tests output


Example timings

MBQN.Rcheck/examples_i386/MBQN-Ex.timings

nameusersystemelapsed
getKminmax000

MBQN.Rcheck/examples_x64/MBQN-Ex.timings

nameusersystemelapsed
getKminmax0.020.000.01