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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:14 -0500 (Thu, 16 Jan 2020).
| Package 155/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocOncoTK 1.7.1 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings
| name | user | system | elapsed | |
| CCLE_DRUG_BROAD | 0.159 | 0.034 | 0.193 | |
| MSIsensor.10k | 0.025 | 0.004 | 0.028 | |
| TcgaMutCounts | 0.000 | 0.001 | 0.001 | |
| TcgaNIndWithAnyMut | 0.001 | 0.000 | 0.000 | |
| add_sym | 0.001 | 0.000 | 0.001 | |
| annotTabs | 0.001 | 0.001 | 0.001 | |
| bindMSI | 0.001 | 0.001 | 0.002 | |
| bipg_tests | 0.520 | 0.012 | 0.538 | |
| brcaMAE | 1.825 | 0.125 | 1.951 | |
| buildPancanSE | 0.001 | 0.000 | 0.001 | |
| cell_70138 | 0.002 | 0.002 | 0.005 | |
| clueDemos | 0.001 | 0.001 | 0.002 | |
| clueServiceNames | 0.001 | 0.001 | 0.001 | |
| darmGBMcls | 0.417 | 0.054 | 0.471 | |
| dingMSI | 0.008 | 0.000 | 0.008 | |
| featIDMapper | 0.001 | 0.000 | 0.000 | |
| fireMSI | 2.278 | 0.403 | 2.682 | |
| get_plates | 0.001 | 0.001 | 0.001 | |
| ggFeatDens | 0.002 | 0.001 | 0.002 | |
| ggFeatureSegs | 0.001 | 0.001 | 0.002 | |
| ggMutDens | 0.001 | 0.001 | 0.001 | |
| icd10_c | 0.132 | 0.046 | 0.177 | |
| k23sig | 0.008 | 0.002 | 0.011 | |
| loadPatel | 0.001 | 0.000 | 0.001 | |
| mc3toGR | 0.002 | 0.000 | 0.002 | |
| molpo_3utr | 1.214 | 0.044 | 1.259 | |
| molpo_5utr | 0.021 | 0.002 | 0.024 | |
| molpo_CDS | 0.078 | 0.024 | 0.101 | |
| molpo_WGS | 0.014 | 0.001 | 0.015 | |
| oncoPrintISB | 0.001 | 0.000 | 0.001 | |
| pancan.clin.varnames | 0.025 | 0.001 | 0.026 | |
| pancan_BQ | 0.001 | 0.000 | 0.001 | |
| pancan_app | 0.001 | 0.000 | 0.000 | |
| pancan_clinicalTabVarnames | 0.001 | 0.000 | 0.001 | |
| pancan_longname | 0.002 | 0.001 | 0.002 | |
| pancan_sampTypeMap | 0.002 | 0.001 | 0.003 | |
| pancan_tabulate | 0.000 | 0.000 | 0.001 | |
| patient_to_tumor_code | 0.010 | 0.000 | 0.011 | |
| pertClasses | 0.001 | 0.000 | 0.001 | |
| pert_70138 | 0.002 | 0.001 | 0.004 | |
| query_clue | 0.001 | 0.000 | 0.002 | |
| small_msi | 0.008 | 0.001 | 0.010 | |
| tumNorSet | 0.001 | 0.000 | 0.001 | |
| utils | 0.324 | 0.021 | 0.349 | |
| viz_msi_raw | 0 | 0 | 0 | |