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BioC 3.5: CHECK report for TCGAbiolinks on malbec2

This page was generated on 2017-08-16 13:16:53 -0400 (Wed, 16 Aug 2017).

Package 1308/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.5.7
Antonio Colaprico
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/TCGAbiolinks
Last Changed Rev: 131796 / Revision: 131943
Last Changed Date: 2017-08-07 20:05:58 -0400 (Mon, 07 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCGAbiolinks
Version: 2.5.7
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz
StartedAt: 2017-08-16 02:36:45 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:50:04 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 798.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TCGAbiolinks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.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 ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.5.7’
* 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 ‘TCGAbiolinks’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 66.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   6.4Mb
    doc   58.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery_clinic: no visible binding for global variable ‘portions’
TCGAanalyze_DEA_Affy: no visible global function definition for
  ‘limmamakeContrasts’
TCGAanalyze_DEA_Affy: no visible global function definition for
  ‘limmacontrasts.fit’
TCGAanalyze_analyseGRN: no visible global function definition for
  ‘knnmi.cross’
TCGAanalyze_networkInference: no visible global function definition for
  ‘c3net’
TCGAanalyze_networkInference: no visible global function definition for
  ‘minet’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
  ‘dNetInduce’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
  ‘dNetPipeline’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
  ‘dCommSignif’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
  ‘visNet’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
Undefined global functions or variables:
  c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
  limmacontrasts.fit limmamakeContrasts minet portions value visNet
* 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 R/sysdata.rda ... 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
GDCquery                19.656  0.168  26.524
TCGAanalyze_DMR         16.168  0.012  16.189
TCGAanalyze_LevelTab    15.260  0.000  15.269
GDCdownload              9.188  0.628  68.741
GDCprepare               8.896  0.212  13.156
TCGAvisualize_oncoprint  8.700  0.136  11.020
TCGAanalyze_DEA          8.692  0.016   8.710
TCGAanalyze_Filtering    8.324  0.000   8.326
TCGAanalyze_survival     6.220  0.012   8.900
GDCprepare_clinic        5.688  0.192   8.463
TCGAanalyze_SurvivalKM   3.020  0.024  10.753
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.


TCGAbiolinks.Rcheck/00install.out:

* installing *source* package ‘TCGAbiolinks’ ...
** 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 (TCGAbiolinks)

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings:

nameusersystemelapsed
GDCdownload 9.188 0.62868.741
GDCprepare 8.896 0.21213.156
GDCprepare_clinic5.6880.1928.463
GDCquery19.656 0.16826.524
GDCquery_Maf1.7400.0763.464
GDCquery_clinic2.2040.0883.731
TCGAVisualize_volcano4.9800.0004.983
TCGAanalyze_DEA8.6920.0168.710
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMR16.168 0.01216.189
TCGAanalyze_EA0.0040.0000.001
TCGAanalyze_EAcomplete2.4200.0002.422
TCGAanalyze_Filtering8.3240.0008.326
TCGAanalyze_LevelTab15.260 0.00015.269
TCGAanalyze_Normalization4.3360.0004.340
TCGAanalyze_Pathview000
TCGAanalyze_SurvivalKM 3.020 0.02410.753
TCGAanalyze_survival6.2200.0128.900
TCGAprepare_Affy0.0040.0000.000
TCGAprepare_elmer0.0040.0000.007
TCGAquery_MatchedCoupledSampleTypes0.0240.0000.026
TCGAquery_SampleTypes0.0000.0000.002
TCGAquery_subtype0.0080.0000.008
TCGAvisualize_EAbarplot2.5280.0002.528
TCGAvisualize_Heatmap2.3160.0042.321
TCGAvisualize_PCA4.5080.0004.509
TCGAvisualize_meanMethylation2.7360.0002.738
TCGAvisualize_oncoprint 8.700 0.13611.020
TCGAvisualize_starburst4.8120.0124.832
calculate.pvalues0.0000.0000.001
diffmean0.0360.0040.038
gaiaCNVplot0.0720.0000.073
getAdjacencyBiogrid0.0040.0000.002
getDataCategorySummary2.1760.0123.165
getGDCprojects0.1280.0040.295
getResults2.2600.0203.215
isServeOK0.1040.0080.273
matchedMetExp2.9320.0444.714