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CHECK report for BiocOncoTK on malbec2

This page was generated on 2019-04-09 11:50:52 -0400 (Tue, 09 Apr 2019).

Package 145/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.3.6
VJ Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BiocOncoTK
Branch: master
Last Commit: 1d6a75a
Last Changed Date: 2019-03-11 23:02:29 -0400 (Mon, 11 Mar 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  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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: BiocOncoTK
Version: 1.3.6
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocOncoTK_1.3.6.tar.gz
StartedAt: 2019-04-08 23:01:25 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:04:46 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 201.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocOncoTK.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocOncoTK_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocOncoTK/DESCRIPTION’ ... OK
* this is package ‘BiocOncoTK’ version ‘1.3.6’
* 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 : <anonymous>: 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 : <anonymous>: no visible binding for global variable
  ‘Consequence’
ggMutDens: no visible binding for global variable ‘project_short_name’
mc3toGR : <anonymous>: no visible binding for global variable
  ‘Consequence’
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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck/00check.log’
for details.



Installation output

BiocOncoTK.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocOncoTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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) (2019-03-18 r76245) -- "Unsuffered Consequences"
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.

> # 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, colMeans, colSums, 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, rowMeans, rowSums,
    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 
  9.746   0.346  10.096 

Example timings

BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.0950.0040.099
TcgaMutCounts0.0000.0000.001
TcgaNIndWithAnyMut000
annotTabs0.0010.0000.000
bindMSI0.0010.0000.001
brcaMAE2.0030.0842.088
buildPancanSE0.0010.0000.001
cell_701380.0010.0000.002
clueDemos0.0000.0000.001
clueServiceNames000
darmGBMcls0.4110.0230.435
dingMSI0.0240.0000.024
featIDMapper0.0000.0000.001
fireMSI1.1140.0961.218
ggFeatDens0.0010.0000.001
ggFeatureSegs0.0010.0000.001
ggMutDens000
icd10_c0.0560.0120.068
loadPatel0.0000.0000.001
mc3toGR0.0000.0010.001
oncoPrintISB0.0000.0010.001
pancan.clin.varnames0.0180.0040.022
pancan_BQ0.0000.0000.001
pancan_app000
pancan_clinicalTabVarnames0.0010.0000.001
pancan_longname0.0010.0000.001
pancan_sampTypeMap0.0000.0020.001
pancan_tabulate0.0000.0010.000
pertClasses0.0000.0010.000
pert_701380.0010.0000.001
query_clue0.0010.0000.001
tumNorSet0.0010.0000.001
utils1.460.021.72