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CHECK report for BiocOncoTK on celaya2

This page was generated on 2020-01-16 13:51:14 -0500 (Thu, 16 Jan 2020).

Package 155/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.7.1
VJ Carey
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/BiocOncoTK
Branch: master
Last Commit: c2deb51
Last Changed Date: 2019-12-19 14:11:38 -0500 (Thu, 19 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  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: BiocOncoTK
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocOncoTK_1.7.1.tar.gz
StartedAt: 2020-01-16 02:09:21 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:21:07 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 706.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocOncoTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocOncoTK_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocOncoTK.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocOncoTK/DESCRIPTION’ ... OK
* this is package ‘BiocOncoTK’ version ‘1.7.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiocOncoTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data        5.1Mb
    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
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocOncoTK.Rcheck/00check.log’
for details.



Installation output

BiocOncoTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocOncoTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (BiocOncoTK)

Tests output

BiocOncoTK.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum


> 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, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2020-01-08
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
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, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2020-01-08
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
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, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2020-01-08
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
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'
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
166.163  13.161 182.715 

Example timings

BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.1590.0340.193
MSIsensor.10k0.0250.0040.028
TcgaMutCounts0.0000.0010.001
TcgaNIndWithAnyMut0.0010.0000.000
add_sym0.0010.0000.001
annotTabs0.0010.0010.001
bindMSI0.0010.0010.002
bipg_tests0.5200.0120.538
brcaMAE1.8250.1251.951
buildPancanSE0.0010.0000.001
cell_701380.0020.0020.005
clueDemos0.0010.0010.002
clueServiceNames0.0010.0010.001
darmGBMcls0.4170.0540.471
dingMSI0.0080.0000.008
featIDMapper0.0010.0000.000
fireMSI2.2780.4032.682
get_plates0.0010.0010.001
ggFeatDens0.0020.0010.002
ggFeatureSegs0.0010.0010.002
ggMutDens0.0010.0010.001
icd10_c0.1320.0460.177
k23sig0.0080.0020.011
loadPatel0.0010.0000.001
mc3toGR0.0020.0000.002
molpo_3utr1.2140.0441.259
molpo_5utr0.0210.0020.024
molpo_CDS0.0780.0240.101
molpo_WGS0.0140.0010.015
oncoPrintISB0.0010.0000.001
pancan.clin.varnames0.0250.0010.026
pancan_BQ0.0010.0000.001
pancan_app0.0010.0000.000
pancan_clinicalTabVarnames0.0010.0000.001
pancan_longname0.0020.0010.002
pancan_sampTypeMap0.0020.0010.003
pancan_tabulate0.0000.0000.001
patient_to_tumor_code0.0100.0000.011
pertClasses0.0010.0000.001
pert_701380.0020.0010.004
query_clue0.0010.0000.002
small_msi0.0080.0010.010
tumNorSet0.0010.0000.001
utils0.3240.0210.349
viz_msi_raw000