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CHECK report for BiocOncoTK on celaya2

This page was generated on 2019-10-16 13:02:29 -0400 (Wed, 16 Oct 2019).

Package 148/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.4.0
VJ Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BiocOncoTK
Branch: RELEASE_3_9
Last Commit: 2cd2204
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 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  ERROR  skipped  skipped 
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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2019-10-16 00:54:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:59:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 298.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocOncoTK.Rcheck
Warnings: 0

Command output

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### 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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  8.7Mb
  sub-directories of 1Mb or more:
    data        3.9Mb
    pamphlets   4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘DBI’
A package should be listed in only one of these fields.
* 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
.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’
checkCache_patel: no visible global function definition for
  ‘BiocFileCache’
chrbounds_basic: no visible global function definition for ‘seqlengths’
ggFeatDens : : no visible binding for global variable
  ‘Consequence’
ggFeatDens: no visible binding for global variable ‘tfstart’
ggFeatureSegs: no visible global function definition for ‘genes’
ggFeatureSegs: no visible binding for global variable ‘symbol’
ggMutDens : : no visible binding for global variable
  ‘Consequence’
ggMutDens: no visible binding for global variable ‘project_short_name’
mc3toGR : : no visible binding for global variable
  ‘Consequence’
rainfall: no visible global function definition for ‘genome’
tumNorSet : : no visible global function definition for
  ‘pancan_SE’
Undefined global functions or variables:
  BiocFileCache Consequence genes genome pancan_SE project_short_name
  seqlengths symbol tfstart
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck/00check.log’
for details.



Installation output

BiocOncoTK.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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")
> 
> proc.time()
   user  system elapsed 
 14.498   1.238  15.705 

Example timings

BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.1260.0200.145
TcgaMutCounts0.0010.0010.001
TcgaNIndWithAnyMut0.0010.0000.000
annotTabs0.0010.0000.001
bindMSI0.0020.0000.002
brcaMAE1.9090.1362.087
buildPancanSE0.0000.0010.001
cell_701380.0020.0010.004
clueDemos0.0020.0010.002
clueServiceNames0.0000.0000.001
darmGBMcls0.4970.0690.566
dingMSI0.0210.0030.024
featIDMapper0.0010.0000.001
fireMSI2.4400.2302.672
ggFeatDens0.0010.0000.001
ggFeatureSegs0.0020.0000.002
ggMutDens0.0010.0000.001
icd10_c0.1470.0430.191
loadPatel0.0010.0010.001
mc3toGR0.0020.0010.002
oncoPrintISB0.0020.0000.002
pancan.clin.varnames0.0240.0010.025
pancan_BQ0.0000.0000.001
pancan_app0.0000.0000.001
pancan_clinicalTabVarnames0.0000.0010.001
pancan_longname0.0010.0010.001
pancan_sampTypeMap0.0030.0010.003
pancan_tabulate0.0010.0000.000
pertClasses0.0010.0000.001
pert_701380.0020.0020.004
query_clue0.0010.0000.001
tumNorSet0.0000.0000.001
utils1.6400.3231.977