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CHECK report for BiocOncoTK on malbec2

This page was generated on 2018-10-17 08:31:40 -0400 (Wed, 17 Oct 2018).

Package 131/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.0.3
VJ Carey
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BiocOncoTK
Branch: RELEASE_3_7
Last Commit: 5f05421
Last Changed Date: 2018-08-24 09:38:44 -0400 (Fri, 24 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocOncoTK
Version: 1.0.3
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiocOncoTK_1.0.3.tar.gz
StartedAt: 2018-10-15 22:47:04 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:48:28 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 84.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocOncoTK.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiocOncoTK_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BiocOncoTK.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.3’
* 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 ... OK
* 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
.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’
rainfall: no visible global function definition for ‘genome’
rainfall: no visible global function definition for ‘ggplot’
rainfall: no visible global function definition for ‘aes’
rainfall: no visible global function definition for ‘geom_point’
rainfall: no visible global function definition for ‘theme’
rainfall: no visible global function definition for ‘element_blank’
rainfall: no visible global function definition for ‘ylab’
rainfall: no visible global function definition for ‘xlab’
rainfall: no visible global function definition for ‘geom_vline’
rainfall: no visible global function definition for
  ‘scale_x_continuous’
rainfall: no visible global function definition for ‘ggtitle’
rainfall: no visible global function definition for ‘geom_text’
Undefined global functions or variables:
  BiocFileCache aes element_blank genome geom_point geom_text
  geom_vline ggplot ggtitle scale_x_continuous seqlengths theme xlab
  ylab
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/BiocOncoTK.Rcheck/00check.log’
for details.



Installation output

BiocOncoTK.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BiocOncoTK
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BiocOncoTK’ ...
** 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
* DONE (BiocOncoTK)

Tests output


Example timings

BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.0760.0120.087
TcgaMutCounts0.0000.0000.001
TcgaNIndWithAnyMut000
annotTabs000
brcaMAE4.5960.1764.784
cell_701380.0000.0000.001
clueDemos0.0040.0000.000
clueServiceNames0.0000.0000.001
darmGBMcls0.3080.0160.326
icd10_c0.0280.0120.041
loadPatel0.0000.0000.001
oncoPrintISB0.0040.0000.001
pancan.clin.varnames0.0120.0000.013
pancan_BQ000
pancan_app0.0000.0000.001
pancan_clinicalTabVarnames0.0000.0000.001
pancan_longname0.0000.0040.000
pancan_sampTypeMap0.0000.0000.001
pancan_tabulate000
pertClasses0.0000.0000.001
pert_701380.0000.0000.001
query_clue0.0000.0040.001
utils0.7800.0360.834