Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-01-21 11:08:42 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 SpidermiR on riesling1


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 1851/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpidermiR 1.25.0  (landing page)
Claudia Cava
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/SpidermiR
git_branch: master
git_last_commit: 52052ec
git_last_commit_date: 2021-10-26 12:26:19 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'MAGeCKFlute' which is not available

Summary

Package: SpidermiR
Version: 1.25.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpidermiR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SpidermiR_1.25.0.tar.gz
StartedAt: 2022-01-20 20:10:15 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:12:20 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 125.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SpidermiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpidermiR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SpidermiR_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SpidermiR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.25.0'
* 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 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:
  'MAGeCKFlute' 'TCGAbiolinks' 'ggplot2' 'gplots' 'grDevices'
  'gridExtra' 'lattice' 'latticeExtra'
  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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
SpidermiRquery_disease          0.61   0.00    8.86
SpidermiRdownload_miRNAvalidate 0.11   0.01   16.51
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.



Installation output

SpidermiR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SpidermiR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
** 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 (SpidermiR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MatrixRider' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'monaLisa' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'motifmatchr' is missing or broken
 done

Tests output


Example timings

SpidermiR.Rcheck/SpidermiR-Ex.timings

nameusersystemelapsed
SpidermiRanalyze_degree_centrality0.020.000.02
SpidermiRanalyze_direct_net000
SpidermiRanalyze_direct_subnetwork0.010.000.02
SpidermiRanalyze_subnetwork_neigh000
SpidermiRdownload_drug_gene1.600.033.50
SpidermiRdownload_miRNAextra_cir0.040.001.42
SpidermiRdownload_miRNAprediction3.330.684.00
SpidermiRdownload_miRNAvalidate 0.11 0.0116.51
SpidermiRdownload_net0.330.021.68
SpidermiRprepare_NET0.500.042.29
SpidermiRquery_disease0.610.008.86
SpidermiRquery_networks_type0.000.000.59
SpidermiRquery_spec_networks0.020.000.33
SpidermiRquery_species0.00.00.2