Back to Multiple platform build/check report for BioC 3.13
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-22 15:05:09 -0400 (Wed, 22 Sep 2021).

CHECK results for BiocOncoTK on tokay2

To the developers/maintainers of the BiocOncoTK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocOncoTK.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 166/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.12.1  (landing page)
VJ Carey
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/BiocOncoTK
git_branch: RELEASE_3_13
git_last_commit: 5b4a389
git_last_commit_date: 2021-06-28 15:44:05 -0400 (Mon, 28 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocOncoTK
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocOncoTK_1.12.1.tar.gz
StartedAt: 2021-09-21 19:48:09 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:59:17 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 668.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocOncoTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocOncoTK_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocOncoTK.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocOncoTK/DESCRIPTION' ... OK
* this is package 'BiocOncoTK' version '1.12.1'
* package encoding: UTF-8
* 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 'BiocOncoTK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data        2.6Mb
    pamphlets   4.5Mb
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ggscat_av: warning in png(file = tempfile()): partial argument match of
  'file' to 'filename'
.flexbi: no visible binding for global variable 'v1'
.flexbi: no visible binding for global variable 'v2'
.rainfall.bq.df: no visible global function definition for 'seqlengths'
.rainfall.maeGRL.df: no visible global function definition for 'genome'
.rainfall.maeGRL.df: no visible global function definition for
  'seqlengths'
acronym_to_system: no visible binding for global variable
  'map_tcga_ncit'
add_sym: no visible global function definition for 'mapIds'
bipg_tests: no visible global function definition for 'new'
checkCache_patel: no visible global function definition for
  'BiocFileCache'
chrbounds_basic: no visible global function definition for 'seqlengths'
ggFeatDens : <anonymous>: no visible binding for global variable
  'Consequence'
ggFeatDens: no visible binding for global variable 'tfstart'
ggFeatureSegs: no visible binding for global variable 'symbol'
ggMutDens : <anonymous>: no visible binding for global variable
  'Consequence'
ggMutDens: no visible binding for global variable 'project_short_name'
ggbox: no visible binding for global variable 'acronym'
ggbox: no visible binding for global variable 'symbol'
ggbox: no visible binding for global variable 'log2ex'
ggbox: no visible binding for global variable 'msicode'
ggscat: no visible binding for global variable 'acronym'
ggscat: no visible binding for global variable 'symbol'
ggscat: no visible binding for global variable 'msival'
ggscat: no visible binding for global variable 'log2ex'
ggscat_av: no visible binding for global variable 'acronym'
ggscat_av: no visible binding for global variable 'symbol'
ggscat_av: no visible binding for global variable 'msival'
ggscat_av: no visible binding for global variable 'tmsi'
ggscat_av: no visible binding for global variable 'log2exa'
mc3toGR : <anonymous>: no visible binding for global variable
  'Consequence'
multiviz: no visible binding for global variable 'acronym'
multiviz: no visible binding for global variable 'msival'
prc: no visible binding for global variable 'acronym'
prc: no visible global function definition for 'right_join'
rainfall: no visible global function definition for 'genome'
tumNorSet : <anonymous>: no visible global function definition for
  'pancan_SE'
Undefined global functions or variables:
  BiocFileCache Consequence acronym genome log2ex log2exa mapIds
  map_tcga_ncit msicode msival new pancan_SE project_short_name
  right_join seqlengths symbol tfstart tmsi v1 v2
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
  Note: found 46 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.13-bioc/meat/BiocOncoTK.Rcheck/00check.log'
for details.



Installation output

BiocOncoTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BiocOncoTK_1.12.1.tar.gz && rm -rf BiocOncoTK.buildbin-libdir && mkdir BiocOncoTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocOncoTK.buildbin-libdir BiocOncoTK_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK_1.12.1.zip && rm BiocOncoTK_1.12.1.tar.gz BiocOncoTK_1.12.1.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
  0 7802k    0 47037    0     0   297k      0  0:00:26 --:--:--  0:00:26  296k
 45 7802k   45 3548k    0     0  3097k      0  0:00:02  0:00:01  0:00:01 3096k
 62 7802k   62 4873k    0     0  2262k      0  0:00:03  0:00:02  0:00:01 2262k
 89 7802k   89 7009k    0     0  2226k      0  0:00:03  0:00:03 --:--:-- 2226k
100 7802k  100 7802k    0     0  2282k      0  0:00:03  0:00:03 --:--:-- 2282k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
* installing *source* package 'BiocOncoTK' ...
** 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 'BiocOncoTK'
    finding HTML links ... done
    CCLE_DRUG_BROAD                         html  
    MSIsensor.10k                           html  
    TcgaMutCounts                           html  
    TcgaNIndWithAnyMut                      html  
    add_sym                                 html  
    annotTabs                               html  
    bindMSI                                 html  
    bipg_tests                              html  
    brcaMAE                                 html  
    buildPancanSE                           html  
    cell_70138                              html  
    clueDemos                               html  
    clueServiceNames                        html  
    darmGBMcls                              html  
    dingMSI                                 html  
    featIDMapper                            html  
    fireMSI                                 html  
    get_plates                              html  
    ggFeatDens                              html  
    ggFeatureSegs                           html  
    ggMutDens                               html  
    icd10_c                                 html  
    k23sig                                  html  
    kang_DNArepair                          html  
    loadPatel                               html  
    log10pl1                                html  
    map_tcga_ncit                           html  
    mc3toGR                                 html  
    molpo_3utr                              html  
    molpo_5utr                              html  
    molpo_CDS                               html  
    molpo_WGS                               html  
    multiviz                                html  
    oncoPrintISB                            html  
    pancan.clin.varnames                    html  
    pancan_BQ                               html  
    finding level-2 HTML links ... done

    pancan_app                              html  
    pancan_clinicalTabVarnames              html  
    pancan_longname                         html  
    pancan_sampTypeMap                      html  
    pancan_tabulate                         html  
    patient_to_tumor_code                   html  
    pertClasses                             html  
    pert_70138                              html  
    query_clue                              html  
    reexports                               html  
    replaceRownames                         html  
    small_msi                               html  
    tumNorSet                               html  
    utils                                   html  
    viz_msi_raw                             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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
* installing *source* package 'BiocOncoTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocOncoTK' as BiocOncoTK_1.12.1.zip
* DONE (BiocOncoTK)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BiocOncoTK' successfully unpacked and MD5 sums checked

Tests output

BiocOncoTK.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> # authentication is so problematic that I am skipping this for now
> library(testthat)
> library(BiocOncoTK)

Attaching package: 'BiocOncoTK'

The following object is masked from 'package:stats':

    filter

> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep


> library(reshape2)
> 
> test_check("BiocOncoTK")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4463 sampleMap rows not in names(experiments)
  removing 4 colData rownames not in sampleMap 'primary'
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4463 sampleMap rows not in names(experiments)
  removing 4 colData rownames not in sampleMap 'primary'
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: SKCM_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4841 sampleMap rows not in names(experiments)
  removing 1 colData rownames not in sampleMap 'primary'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  12.79    1.34  139.12 

BiocOncoTK.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> # authentication is so problematic that I am skipping this for now
> library(testthat)
> library(BiocOncoTK)

Attaching package: 'BiocOncoTK'

The following object is masked from 'package:stats':

    filter

> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep


> library(reshape2)
> 
> test_check("BiocOncoTK")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4463 sampleMap rows not in names(experiments)
  removing 4 colData rownames not in sampleMap 'primary'
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4463 sampleMap rows not in names(experiments)
  removing 4 colData rownames not in sampleMap 'primary'
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-05-18
Working on: SKCM_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 4841 sampleMap rows not in names(experiments)
  removing 1 colData rownames not in sampleMap 'primary'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  13.87    0.75  149.73 

Example timings

BiocOncoTK.Rcheck/examples_i386/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.110.000.10
MSIsensor.10k0.030.000.04
TcgaMutCounts000
TcgaNIndWithAnyMut000
add_sym000
annotTabs000
bindMSI000
bipg_tests1.000.001.03
brcaMAE1.250.071.33
buildPancanSE000
cell_70138000
clueDemos000
clueServiceNames000
darmGBMcls0.390.000.39
dingMSI000
featIDMapper000
fireMSI0.770.271.03
get_plates000
ggFeatDens000
ggFeatureSegs000
ggMutDens000
icd10_c0.000.010.01
k23sig0.020.000.02
loadPatel000
mc3toGR000
molpo_3utr0.080.000.08
molpo_5utr0.030.000.03
molpo_CDS0.090.000.10
molpo_WGS0.010.000.01
oncoPrintISB000
pancan.clin.varnames0.000.020.02
pancan_BQ000
pancan_app000
pancan_clinicalTabVarnames000
pancan_longname0.000.000.02
pancan_sampTypeMap0.000.020.01
pancan_tabulate000
patient_to_tumor_code000
pertClasses000
pert_70138000
query_clue000
small_msi000
tumNorSet000
utils0.160.040.78
viz_msi_raw000

BiocOncoTK.Rcheck/examples_x64/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.090.020.11
MSIsensor.10k0.020.000.01
TcgaMutCounts000
TcgaNIndWithAnyMut000
add_sym000
annotTabs000
bindMSI000
bipg_tests0.250.000.25
brcaMAE1.250.041.29
buildPancanSE000
cell_70138000
clueDemos000
clueServiceNames000
darmGBMcls0.250.030.29
dingMSI0.020.000.01
featIDMapper000
fireMSI0.790.020.81
get_plates000
ggFeatDens000
ggFeatureSegs000
ggMutDens000
icd10_c0.020.020.04
k23sig000
loadPatel000
mc3toGR000
molpo_3utr0.860.000.85
molpo_5utr0.010.000.02
molpo_CDS0.070.000.06
molpo_WGS0.030.000.03
oncoPrintISB000
pancan.clin.varnames000
pancan_BQ000
pancan_app000
pancan_clinicalTabVarnames000
pancan_longname000
pancan_sampTypeMap000
pancan_tabulate000
patient_to_tumor_code0.010.000.02
pertClasses000
pert_70138000
query_clue000
small_msi000
tumNorSet000
utils0.160.010.17
viz_msi_raw000