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This page was generated on 2021-10-13 15:05:40 -0400 (Wed, 13 Oct 2021).

CHECK results for SpidermiR on tokay2

To the developers/maintainers of the SpidermiR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpidermiR.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 1825/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpidermiR 1.22.1  (landing page)
Claudia Cava
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/SpidermiR
git_branch: RELEASE_3_13
git_last_commit: 45680ec
git_last_commit_date: 2021-06-16 06:21:54 -0400 (Wed, 16 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: SpidermiR
Version: 1.22.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SpidermiR_1.22.1.tar.gz
StartedAt: 2021-10-13 05:41:04 -0400 (Wed, 13 Oct 2021)
EndedAt: 2021-10-13 05:44:13 -0400 (Wed, 13 Oct 2021)
EllapsedTime: 189.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SpidermiR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SpidermiR_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SpidermiR.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 'SpidermiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpidermiR' version '1.22.1'
* 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 'SpidermiR' 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:
  'MAGeCKFlute' 'TCGAbiolinks' 'ggplot2' 'gplots' 'grDevices'
  'gridExtra' 'lattice' 'latticeExtra' 'networkD3' 'visNetwork'
  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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SpidermiR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpidermiRdownload_miRNAvalidate
> ### Title: Download miRNA validated database
> ### Aliases: SpidermiRdownload_miRNAvalidate
> 
> ### ** Examples
> 
> list<-SpidermiRdownload_miRNAvalidate(validated)
trying URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip'
Warning in download.file(.url_cache$get("miRwalk"), temp) :
  cannot open URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip': HTTP status was '404 Not Found'
Error in download.file(.url_cache$get("miRwalk"), temp) : 
  cannot open URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip'
Calls: SpidermiRdownload_miRNAvalidate -> download.file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SpidermiR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpidermiRdownload_miRNAvalidate
> ### Title: Download miRNA validated database
> ### Aliases: SpidermiRdownload_miRNAvalidate
> 
> ### ** Examples
> 
> list<-SpidermiRdownload_miRNAvalidate(validated)
trying URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip'
Warning in download.file(.url_cache$get("miRwalk"), temp) :
  cannot open URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip': HTTP status was '404 Not Found'
Error in download.file(.url_cache$get("miRwalk"), temp) : 
  cannot open URL 'http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/downloads/vtm/hsa-vtm-gene.rdata.zip'
Calls: SpidermiRdownload_miRNAvalidate -> download.file
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-3.13-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.


Installation output

SpidermiR.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/SpidermiR_1.22.1.tar.gz && rm -rf SpidermiR.buildbin-libdir && mkdir SpidermiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpidermiR.buildbin-libdir SpidermiR_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SpidermiR_1.22.1.zip && rm SpidermiR_1.22.1.tar.gz SpidermiR_1.22.1.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 13680  100 13680    0     0   114k      0 --:--:-- --:--:-- --:--:--  115k

install for i386

* installing *source* package 'SpidermiR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SpidermiR'
    finding HTML links ... done
    SpidermiRanalyze_degree_centrality      html  
    SpidermiRanalyze_direct_net             html  
    SpidermiRanalyze_direct_subnetwork      html  
    SpidermiRanalyze_subnetwork_neigh       html  
    SpidermiRdownload_drug_gene             html  
    SpidermiRdownload_miRNAextra_cir        html  
    SpidermiRdownload_miRNAprediction       html  
    SpidermiRdownload_miRNAvalidate         html  
    SpidermiRdownload_net                   html  
    SpidermiRprepare_NET                    html  
    SpidermiRquery_disease                  html  
    SpidermiRquery_networks_type            html  
    SpidermiRquery_spec_networks            html  
    SpidermiRquery_species                  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 'SpidermiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpidermiR' as SpidermiR_1.22.1.zip
* DONE (SpidermiR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SpidermiR' successfully unpacked and MD5 sums checked

Tests output


Example timings

SpidermiR.Rcheck/examples_i386/SpidermiR-Ex.timings

nameusersystemelapsed
SpidermiRanalyze_degree_centrality000
SpidermiRanalyze_direct_net0.020.000.02
SpidermiRanalyze_direct_subnetwork0.010.000.02
SpidermiRanalyze_subnetwork_neigh000
SpidermiRdownload_drug_gene15.82 0.1716.61
SpidermiRdownload_miRNAextra_cir3.871.115.39
SpidermiRdownload_miRNAprediction3.800.664.45

SpidermiR.Rcheck/examples_x64/SpidermiR-Ex.timings

nameusersystemelapsed
SpidermiRanalyze_degree_centrality000
SpidermiRanalyze_direct_net000
SpidermiRanalyze_direct_subnetwork000
SpidermiRanalyze_subnetwork_neigh000
SpidermiRdownload_drug_gene12.97 0.1413.75
SpidermiRdownload_miRNAextra_cir2.901.084.35
SpidermiRdownload_miRNAprediction4.160.354.53