VJ Carey
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BiocOncoTK |
| git_branch: master |
| git_last_commit: d1fad8e |
| git_last_commit_date: 2022-01-14 11:42:50 -0400 (Fri, 14 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BiocOncoTK package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocOncoTK.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 161/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocOncoTK 1.15.1 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: BiocOncoTK |
| Version: 1.15.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocOncoTK.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocOncoTK_1.15.1.tar.gz |
| StartedAt: 2022-03-17 18:32:38 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:38:24 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 346.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocOncoTK.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocOncoTK.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocOncoTK_1.15.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BiocOncoTK.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocOncoTK/DESCRIPTION' ... OK
* this is package 'BiocOncoTK' version '1.15.1'
* 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 whether package 'BiocOncoTK' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'BiocOncoTK'
See 'D:/biocbuild/bbs-3.15-bioc/meat/BiocOncoTK.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 2.5Mb
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
Error loading dataset 'brcaMAE':
Error in get_Nindex_lengths(x@index, dim(x@seed)) :
length(Nindex) == length(dim) is not TRUE
Note: found 46 marked UTF-8 strings
* checking LazyData ... OK
* 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: 1 WARNING, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/BiocOncoTK.Rcheck/00check.log'
for details.
BiocOncoTK.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'BiocOncoTK'
** help
*** installing help indices
converting help for package 'BiocOncoTK'
finding HTML links ... done
CCLE_DRUG_BROAD html
MSIsensor.10k html
TcgaMutCounts html
TcgaNIndWithAnyMut html
add_sym html
annotTabs html
bindMSI html
bipg_tests html
brcaMAE html
buildPancanSE html
cell_70138 html
clueDemos html
clueServiceNames html
darmGBMcls html
dingMSI html
featIDMapper html
fireMSI html
get_plates html
ggFeatDens html
ggFeatureSegs html
ggMutDens html
icd10_c html
k23sig html
kang_DNArepair html
loadPatel html
log10pl1 html
map_tcga_ncit html
mc3toGR html
molpo_3utr html
molpo_5utr html
molpo_CDS html
molpo_WGS html
multiviz html
oncoPrintISB html
pancan.clin.varnames html
pancan_BQ html
finding level-2 HTML links ... done
pancan_app html
pancan_clinicalTabVarnames html
pancan_longname html
pancan_sampTypeMap html
pancan_tabulate html
patient_to_tumor_code html
pertClasses html
pert_70138 html
query_clue html
reexports html
replaceRownames html
small_msi html
tumNorSet html
utils html
viz_msi_raw html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'BiocOncoTK'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'BiocOncoTK'
** testing if installed package keeps a record of temporary installation path
* DONE (BiocOncoTK)
Making 'packages.html' ... done
BiocOncoTK.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Warning message:
replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'BiocOncoTK'
> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: DelayedArray
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
> library(reshape2)
>
> test_check("BiocOncoTK")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-03-16
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
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
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-03-16
Working on: BLCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BLCA_sampleMap-20160128
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
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-03-16
Working on: SKCM_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: SKCM_sampleMap-20160128
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'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
>
> proc.time()
user system elapsed
11.85 0.87 91.28
BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings
| name | user | system | elapsed | |
| CCLE_DRUG_BROAD | 0.11 | 0.00 | 0.11 | |
| MSIsensor.10k | 0.03 | 0.00 | 0.03 | |
| TcgaMutCounts | 0 | 0 | 0 | |
| TcgaNIndWithAnyMut | 0 | 0 | 0 | |
| add_sym | 0 | 0 | 0 | |
| annotTabs | 0 | 0 | 0 | |
| bindMSI | 0 | 0 | 0 | |
| bipg_tests | 0.29 | 0.02 | 0.30 | |
| brcaMAE | 1.06 | 0.04 | 1.11 | |
| buildPancanSE | 0 | 0 | 0 | |
| cell_70138 | 0 | 0 | 0 | |
| clueDemos | 0 | 0 | 0 | |
| clueServiceNames | 0 | 0 | 0 | |
| darmGBMcls | 0.31 | 0.00 | 0.31 | |
| dingMSI | 0 | 0 | 0 | |
| featIDMapper | 0 | 0 | 0 | |
| fireMSI | 0.79 | 0.10 | 0.89 | |
| get_plates | 0 | 0 | 0 | |
| ggFeatDens | 0 | 0 | 0 | |
| ggFeatureSegs | 0 | 0 | 0 | |
| ggMutDens | 0 | 0 | 0 | |
| icd10_c | 0.03 | 0.00 | 0.03 | |
| k23sig | 0 | 0 | 0 | |
| loadPatel | 0 | 0 | 0 | |
| mc3toGR | 0 | 0 | 0 | |
| molpo_3utr | 0.83 | 0.00 | 0.83 | |
| molpo_5utr | 0.02 | 0.00 | 0.02 | |
| molpo_CDS | 0.06 | 0.02 | 0.08 | |
| molpo_WGS | 0.02 | 0.00 | 0.01 | |
| oncoPrintISB | 0 | 0 | 0 | |
| pancan.clin.varnames | 0 | 0 | 0 | |
| pancan_BQ | 0 | 0 | 0 | |
| pancan_app | 0 | 0 | 0 | |
| pancan_clinicalTabVarnames | 0 | 0 | 0 | |
| pancan_longname | 0 | 0 | 0 | |
| pancan_sampTypeMap | 0.01 | 0.00 | 0.02 | |
| pancan_tabulate | 0 | 0 | 0 | |
| patient_to_tumor_code | 0 | 0 | 0 | |
| pertClasses | 0 | 0 | 0 | |
| pert_70138 | 0.00 | 0.01 | 0.01 | |
| query_clue | 0 | 0 | 0 | |
| small_msi | 0 | 0 | 0 | |
| tumNorSet | 0 | 0 | 0 | |
| utils | 0.14 | 0.03 | 0.18 | |
| viz_msi_raw | 0 | 0 | 0 | |