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CHECK report for TCGAbiolinks on tokay2

This page was generated on 2019-10-16 12:33:51 -0400 (Wed, 16 Oct 2019).

Package 1631/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.12.6
Antonio Colaprico
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TCGAbiolinks
Branch: RELEASE_3_9
Last Commit: 7c927a69
Last Changed Date: 2019-09-05 08:13:22 -0400 (Thu, 05 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCGAbiolinks
Version: 2.12.6
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.12.6.tar.gz
StartedAt: 2019-10-16 07:30:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:04:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 2015.1 seconds
RetCode: 0
Status:  OK  
CheckDir: TCGAbiolinks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.12.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.12.6'
* 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 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   3.6Mb
* 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
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'
readIDATDNAmethylation: no visible global function definition for
  'openSesame'
Undefined global functions or variables:
  Tumor.purity barcode c3net clinical coordinates dCommSignif
  dNetInduce dNetPipeline exon knnmi.cross limmacontrasts.fit
  limmamakeContrasts minet openSesame 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
TCGAanalyze_DMR           21.42   0.49   21.91
TCGAanalyze_LevelTab      20.25   0.02   20.26
TCGAanalyze_DEA           14.10   0.34   14.44
TCGAanalyze_Filtering     10.90   0.00   10.91
GDCprepare_clinic         10.36   0.31   57.76
GDCdownload                6.06   0.18   40.44
TCGAvisualize_PCA          5.37   0.01    5.39
TCGAanalyze_Stemness       5.36   0.00    5.36
TCGAanalyze_Normalization  5.10   0.00    5.10
getSampleFilesSummary      3.47   0.09    8.57
getManifest                3.32   0.01    7.65
GDCquery                   2.69   0.00    7.21
matchedMetExp              2.59   0.02    7.68
getResults                 2.40   0.02    6.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
TCGAanalyze_DMR           34.78   0.11   35.66
TCGAanalyze_LevelTab      20.77   0.10   20.95
TCGAanalyze_DEA           14.78   0.06   16.18
TCGAanalyze_Filtering     13.18   0.00   13.19
GDCprepare_clinic         11.78   0.17   60.86
TCGAvisualize_PCA          6.18   0.00    6.17
TCGAanalyze_Stemness       5.45   0.00    5.46
TCGAanalyze_Normalization  5.42   0.00    5.42
GDCdownload                4.87   0.13   38.39
matchedMetExp              3.44   0.04    9.23
getManifest                3.35   0.00    8.37
getSampleFilesSummary      3.02   0.06    8.28
GDCquery                   2.95   0.03    7.45
getResults                 2.97   0.00    8.69
getDataCategorySummary     2.20   0.06    6.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.



Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TCGAbiolinks_2.12.6.tar.gz && rm -rf TCGAbiolinks.buildbin-libdir && mkdir TCGAbiolinks.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.12.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks_2.12.6.zip && rm TCGAbiolinks_2.12.6.tar.gz TCGAbiolinks_2.12.6.zip
###
##############################################################################
##############################################################################


  % 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 6477k  100 6477k    0     0  43.8M      0 --:--:-- --:--:-- --:--:-- 45.8M

install for i386

* installing *source* package 'TCGAbiolinks' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAbiolinks'
    finding HTML links ... done
    BRCA_rnaseqv2                           html  
    GDCdownload                             html  
    GDCprepare                              html  
    GDCprepare_clinic                       html  
    GDCquery                                html  
    GDCquery_ATAC_seq                       html  
    GDCquery_Maf                            html  
    GDCquery_clinic                         html  
    GeneSplitRegulon                        html  
    GenesCutID                              html  
    PCBC_stemSig                            html  
    PanCancerAtlas_subtypes                 html  
    TCGAVisualize_volcano                   html  
    TCGA_MolecularSubtype                   html  
    TCGAanalyze_Clustering                  html  
    TCGAanalyze_DEA                         html  
    TCGAanalyze_DEA_Affy                    html  
    TCGAanalyze_DMR                         html  
    TCGAanalyze_EA                          html  
    TCGAanalyze_EAcomplete                  html  
    TCGAanalyze_Filtering                   html  
    TCGAanalyze_LevelTab                    html  
    TCGAanalyze_Normalization               html  
    TCGAanalyze_Pathview                    html  
    TCGAanalyze_Preprocessing               html  
    TCGAanalyze_Stemness                    html  
    TCGAanalyze_SurvivalKM                  html  
    TCGAanalyze_analyseGRN                  html  
    TCGAanalyze_networkInference            html  
    TCGAanalyze_survival                    html  
    TCGAbatch_Correction                    html  
    TCGAbiolinks                            html  
    TCGAprepare_Affy                        html  
    TCGAquery_MatchedCoupledSampleTypes     html  
    TCGAquery_SampleTypes                   html  
    TCGAquery_recount2                      html  
    TCGAquery_subtype                       html  
    TCGAtumor_purity                        html  
    TCGAvisualize_BarPlot                   html  
    TCGAvisualize_EAbarplot                 html  
    TCGAvisualize_Heatmap                   html  
    TCGAvisualize_PCA                       html  
    TCGAvisualize_SurvivalCoxNET            html  
    TCGAvisualize_meanMethylation           html  
    TCGAvisualize_oncoprint                 html  
    TCGAvisualize_starburst                 html  
    TabSubtypesCol_merged                   html  
    Tumor.purity                            html  
    UseRaw_afterFilter                      html  
    batch.info                              html  
    bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf
                                            html  
    calculate.pvalues                       html  
    chol_maf                                html  
    clinBRCA                                html  
    clinical.biotab                         html  
    colDataPrepare                          html  
    dataBRCA                                html  
    dataDEGsFiltLevel                       html  
    dataREAD                                html  
    dataREAD_df                             html  
    diffmean                                html  
    gaiaCNVplot                             html  
    gbm.exp.harmonized                      html  
    gbm.exp.legacy                          html  
    geneInfo                                html  
    geneInfoHT                              html  
    get.GRCh.bioMart                        html  
    getAdjacencyBiogrid                     html  
    getDataCategorySummary                  html  
    getGDCInfo                              html  
    getGDCprojects                          html  
    getGistic                               html  
    getManifest                             html  
    getResults                              html  
    getSampleFilesSummary                   html  
    getTSS                                  html  
    get_IDs                                 html  
    ggbiplot                                html  
    isServeOK                               html  
    matchedMetExp                           html  
    met.gbm.27k                             html  
    msi_results                             html  
    pancan2018                              html  
    tabSurvKMcompleteDEGs                   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 'TCGAbiolinks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.12.6.zip
* DONE (TCGAbiolinks)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TCGAbiolinks' successfully unpacked and MD5 sums checked

Tests output

TCGAbiolinks.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 209.53    5.07  531.43 

TCGAbiolinks.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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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  |======================================================================| 100%
[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 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 189.28    1.96  527.48 

Example timings

TCGAbiolinks.Rcheck/examples_i386/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload 6.06 0.1840.44
GDCprepare000
GDCprepare_clinic10.36 0.3157.76
GDCquery2.690.007.21
GDCquery_ATAC_seq000
GDCquery_Maf000
GDCquery_clinic1.110.022.63
PanCancerAtlas_subtypes0.030.000.03
TCGAVisualize_volcano0.320.000.33
TCGA_MolecularSubtype0.440.000.43
TCGAanalyze_DEA14.10 0.3414.44
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMR21.42 0.4921.91
TCGAanalyze_EA000
TCGAanalyze_EAcomplete3.100.013.11
TCGAanalyze_Filtering10.90 0.0010.91
TCGAanalyze_LevelTab20.25 0.0220.26
TCGAanalyze_Normalization5.10.05.1
TCGAanalyze_Pathview000
TCGAanalyze_Stemness5.360.005.36
TCGAanalyze_SurvivalKM0.070.000.08
TCGAanalyze_survival2.740.052.78
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes000
TCGAquery_SampleTypes000
TCGAquery_recount2000
TCGAquery_subtype0.010.000.01
TCGAtumor_purity0.150.000.14
TCGAvisualize_EAbarplot2.600.002.61
TCGAvisualize_Heatmap1.180.001.17
TCGAvisualize_PCA5.370.015.39
TCGAvisualize_meanMethylation2.670.022.71
TCGAvisualize_oncoprint000
TCGAvisualize_starburst000
UseRaw_afterFilter000
calculate.pvalues000
colDataPrepare000
diffmean0.080.000.08
gaiaCNVplot0.030.000.03
getAdjacencyBiogrid000
getDataCategorySummary1.570.014.81
getGDCInfo0.000.020.17
getGDCprojects0.030.000.16
getManifest3.320.017.65
getResults2.400.026.30
getSampleFilesSummary3.470.098.57
getTSS000
isServeOK0.000.000.18
matchedMetExp2.590.027.68

TCGAbiolinks.Rcheck/examples_x64/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload 4.87 0.1338.39
GDCprepare000
GDCprepare_clinic11.78 0.1760.86
GDCquery2.950.037.45
GDCquery_ATAC_seq000
GDCquery_Maf000
GDCquery_clinic0.940.042.55
PanCancerAtlas_subtypes0.000.010.01
TCGAVisualize_volcano0.390.000.39
TCGA_MolecularSubtype0.340.000.35
TCGAanalyze_DEA14.78 0.0616.18
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMR34.78 0.1135.66
TCGAanalyze_EA000
TCGAanalyze_EAcomplete3.180.003.17
TCGAanalyze_Filtering13.18 0.0013.19
TCGAanalyze_LevelTab20.77 0.1020.95
TCGAanalyze_Normalization5.420.005.42
TCGAanalyze_Pathview000
TCGAanalyze_Stemness5.450.005.46
TCGAanalyze_SurvivalKM0.080.000.07
TCGAanalyze_survival2.910.002.91
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes000
TCGAquery_SampleTypes000
TCGAquery_recount2000
TCGAquery_subtype000
TCGAtumor_purity0.160.000.16
TCGAvisualize_EAbarplot2.640.012.65
TCGAvisualize_Heatmap1.430.021.46
TCGAvisualize_PCA6.180.006.17
TCGAvisualize_meanMethylation3.260.013.28
TCGAvisualize_oncoprint000
TCGAvisualize_starburst000
UseRaw_afterFilter000
calculate.pvalues000
colDataPrepare000
diffmean0.170.000.17
gaiaCNVplot0.040.020.05
getAdjacencyBiogrid0.010.000.02
getDataCategorySummary2.200.066.42
getGDCInfo0.020.000.18
getGDCprojects0.020.000.18
getManifest3.350.008.37
getResults2.970.008.69
getSampleFilesSummary3.020.068.28
getTSS000
isServeOK0.000.000.16
matchedMetExp3.440.049.23