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CHECK report for TCGAbiolinks on malbec1

This page was generated on 2019-04-16 11:51:32 -0400 (Tue, 16 Apr 2019).

Package 1546/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.10.5
Antonio Colaprico
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TCGAbiolinks
Branch: RELEASE_3_8
Last Commit: c51253f
Last Changed Date: 2019-03-20 10:11:14 -0400 (Wed, 20 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCGAbiolinks
Version: 2.10.5
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAbiolinks_2.10.5.tar.gz
StartedAt: 2019-04-16 03:22:29 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:40:55 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 1106.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: TCGAbiolinks.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAbiolinks_2.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.10.5’
* 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  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   3.5Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘purrr’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘move’
* 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: no visible binding for global variable ‘barcode’
TCGAanalyze_DEA: no visible binding for global variable ‘clinical’
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’
TCGAquery_recount2: no visible binding for global variable ‘rse_gene’
TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
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’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
  ‘coordinates’
Undefined global functions or variables:
  Tumor.purity barcode c3net clinical coordinates dCommSignif
  dNetInduce dNetPipeline exon knnmi.cross limmacontrasts.fit
  limmamakeContrasts minet portions rse_gene 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
TCGAanalyze_LevelTab      20.620  0.032  20.675
TCGAanalyze_DMR           18.476  0.020  18.505
GDCprepare_clinic         10.588  0.364  53.740
TCGAanalyze_DEA           10.600  0.180  10.786
TCGAanalyze_Filtering     10.384  0.004  10.396
GDCdownload                7.296  0.220  35.555
TCGAvisualize_PCA          7.060  0.000  10.973
GDCquery_clinic            6.128  0.088   4.635
TCGAanalyze_Normalization  6.208  0.000   6.214
GDCprepare                 5.256  0.308   8.216
matchedMetExp              3.352  0.060   9.080
getResults                 3.184  0.032   9.090
getSampleFilesSummary      2.800  0.100   8.602
GDCquery                   2.680  0.036   7.284
getManifest                2.520  0.020   7.932
getDataCategorySummary     2.248  0.020   7.046
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.



Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TCGAbiolinks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TCGAbiolinks’ ...
** R
Warning in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  :
  internal error 10 in R_compress3
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAbiolinks)

Tests output

TCGAbiolinks.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TCGAbiolinks)
> 
> test_check("TCGAbiolinks")

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[1] "I need about  1 minute to finish complete  Enrichment analysis GO[BP,MF,CC] and Pathways... "
[1] "GO Enrichment Analysis BP completed....done"
[1] "GO Enrichment Analysis MF completed....done"
[1] "GO Enrichment Analysis CC completed....done"
[1] "Pathway Enrichment Analysis completed....done"
  groups      Mean    Median       Max       Min
1     TP 0.3590198 0.3601768 0.4099433 0.3240056
  groups      Mean    Median       Max       Min
1     TP 0.3590198 0.3601768 0.4099433 0.3240056
  groups      Mean    Median       Max       Min
1   LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2   LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3   LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4   LGm5 0.3481159 0.3524203 0.3608853 0.3267376
     LGm1 LGm2      LGm4      LGm5
LGm1   NA   NA        NA        NA
LGm2   NA   NA        NA        NA
LGm4   NA   NA        NA 0.9217168
LGm5   NA   NA 0.9217168        NA
  groups      Mean    Median       Max       Min
1   LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2   LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3   LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4   LGm5 0.3481159 0.3524203 0.3608853 0.3267376
     LGm1 LGm2      LGm4      LGm5
LGm1   NA   NA        NA        NA
LGm2   NA   NA        NA        NA
LGm4   NA   NA        NA 0.9217168
LGm5   NA   NA 0.9217168        NA
  groups      Mean    Median       Max       Min
1   LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2   LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3   LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4   LGm5 0.3481159 0.3524203 0.3608853 0.3267376
     LGm1 LGm2      LGm4      LGm5
LGm1   NA   NA        NA        NA
LGm2   NA   NA        NA        NA
LGm4   NA   NA        NA 0.9217168
LGm5   NA   NA 0.9217168        NA
  groups      Mean    Median       Max       Min
1  alive 0.3594683 0.3594683 0.3594683 0.3594683
2   dead 0.3589557 0.3608853 0.4099433 0.3240056
      alive dead
alive    NA   NA
dead     NA   NA
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 67 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
192.184   1.656 537.370 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload 7.296 0.22035.555
GDCprepare5.2560.3088.216
GDCprepare_clinic10.588 0.36453.740
GDCquery2.6800.0367.284
GDCquery_ATAC_seq000
GDCquery_Maf000
GDCquery_clinic6.1280.0884.635
PanCancerAtlas_subtypes0.0200.0000.023
TCGAVisualize_volcano0.4720.0000.471
TCGA_MolecularSubtype0.5120.0000.512
TCGAanalyze_DEA10.600 0.18010.786
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMR18.476 0.02018.505
TCGAanalyze_EA000
TCGAanalyze_EAcomplete3.5440.0003.549
TCGAanalyze_Filtering10.384 0.00410.396
TCGAanalyze_LevelTab20.620 0.03220.675
TCGAanalyze_Normalization6.2080.0006.214
TCGAanalyze_Pathview000
TCGAanalyze_SurvivalKM0.1400.0000.138
TCGAanalyze_survival2.4840.0042.488
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0040.0000.003
TCGAquery_SampleTypes0.0000.0000.001
TCGAquery_recount2000
TCGAquery_subtype0.0120.0000.011
TCGAtumor_purity0.1600.0000.159
TCGAvisualize_EAbarplot3.9200.0083.933
TCGAvisualize_Heatmap1.6520.0001.654
TCGAvisualize_PCA 7.060 0.00010.973
TCGAvisualize_meanMethylation3.6040.0563.723
TCGAvisualize_oncoprint0.0000.0000.001
TCGAvisualize_starburst0.0040.0000.000
UseRaw_afterFilter000
calculate.pvalues000
colDataPrepare000
diffmean0.0520.0000.052
gaiaCNVplot0.0240.0000.024
getAdjacencyBiogrid0.0040.0000.002
getDataCategorySummary2.2480.0207.046
getGDCInfo0.1520.0120.537
getGDCprojects0.1560.0040.464
getManifest2.5200.0207.932
getResults3.1840.0329.090
getSampleFilesSummary2.8000.1008.602
getTSS000
isServeOK0.2680.0080.543
matchedMetExp3.3520.0609.080