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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:14:32 -0400 (Wed, 16 Oct 2019).
| Package 148/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocOncoTK 1.4.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| 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 | |
| Package: BiocOncoTK |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2019-10-16 00:05:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:08:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 192.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocOncoTK.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck/00check.log’
for details.
BiocOncoTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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-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, 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
8.520 0.366 8.888
BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings
| name | user | system | elapsed | |
| CCLE_DRUG_BROAD | 0.073 | 0.000 | 0.073 | |
| TcgaMutCounts | 0 | 0 | 0 | |
| TcgaNIndWithAnyMut | 0.001 | 0.000 | 0.000 | |
| annotTabs | 0 | 0 | 0 | |
| bindMSI | 0.001 | 0.000 | 0.001 | |
| brcaMAE | 1.252 | 0.039 | 1.342 | |
| buildPancanSE | 0.001 | 0.000 | 0.001 | |
| cell_70138 | 0.002 | 0.000 | 0.002 | |
| clueDemos | 0.001 | 0.000 | 0.001 | |
| clueServiceNames | 0 | 0 | 0 | |
| darmGBMcls | 0.393 | 0.012 | 0.405 | |
| dingMSI | 0.017 | 0.004 | 0.021 | |
| featIDMapper | 0.000 | 0.000 | 0.001 | |
| fireMSI | 0.878 | 0.071 | 0.949 | |
| ggFeatDens | 0 | 0 | 0 | |
| ggFeatureSegs | 0 | 0 | 0 | |
| ggMutDens | 0 | 0 | 0 | |
| icd10_c | 0.031 | 0.008 | 0.039 | |
| loadPatel | 0.000 | 0.000 | 0.001 | |
| mc3toGR | 0.000 | 0.000 | 0.001 | |
| oncoPrintISB | 0 | 0 | 0 | |
| pancan.clin.varnames | 0.011 | 0.001 | 0.012 | |
| pancan_BQ | 0 | 0 | 0 | |
| pancan_app | 0 | 0 | 0 | |
| pancan_clinicalTabVarnames | 0 | 0 | 0 | |
| pancan_longname | 0.001 | 0.000 | 0.001 | |
| pancan_sampTypeMap | 0.001 | 0.000 | 0.001 | |
| pancan_tabulate | 0 | 0 | 0 | |
| pertClasses | 0.001 | 0.000 | 0.001 | |
| pert_70138 | 0.001 | 0.000 | 0.001 | |
| query_clue | 0.001 | 0.000 | 0.001 | |
| tumNorSet | 0 | 0 | 0 | |
| utils | 1.291 | 0.048 | 1.347 | |