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BioC 3.5: CHECK report for goSTAG on malbec2

This page was generated on 2017-08-16 13:18:09 -0400 (Wed, 16 Aug 2017).

Package 579/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goSTAG 1.0.1
Brian D. Bennett
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/goSTAG
Last Changed Rev: 130111 / Revision: 131943
Last Changed Date: 2017-06-05 12:41:35 -0400 (Mon, 05 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goSTAG
Version: 1.0.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goSTAG_1.0.1.tar.gz
StartedAt: 2017-08-15 23:34:37 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:39:36 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 299.2 seconds
RetCode: 0
Status:  OK 
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goSTAG_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/goSTAG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goSTAG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goSTAG’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘goSTAG’ 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
groupClusters                 38.416  0.028  38.461
performGOEnrichment           36.048  0.004  36.074
plotHeatmap                   35.768  0.024  35.809
performHierarchicalClustering 35.452  0.020  35.492
goSTAG-package                35.416  0.020  35.451
annotateClusters              34.688  0.024  34.734
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: OK

goSTAG.Rcheck/00install.out:

* installing *source* package ‘goSTAG’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (goSTAG)

goSTAG.Rcheck/goSTAG-Ex.timings:

nameusersystemelapsed
annotateClusters34.688 0.02434.734
goSTAG-package35.416 0.02035.451
goSTAG_example_gene_lists0.0000.0000.002
goSTAG_go_genes_human0.0720.0040.077
goSTAG_go_genes_mouse0.2480.0040.251
goSTAG_go_genes_rat0.0560.0080.065
groupClusters38.416 0.02838.461
loadGOTerms0.3760.0000.376
loadGeneLists0.0040.0000.005
performGOEnrichment36.048 0.00436.074
performHierarchicalClustering35.452 0.02035.492
plotHeatmap35.768 0.02435.809
rat_cancer_therapeutics_gene_lists0.0040.0000.005