VJ Carey
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BiocOncoTK |
| git_branch: RELEASE_3_17 |
| git_last_commit: ceb097d |
| git_last_commit_date: 2023-04-25 11:01:44 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 182/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocOncoTK 1.20.0 (landing page) VJ Carey
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BiocOncoTK package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BiocOncoTK |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocOncoTK_1.20.0.tar.gz |
| StartedAt: 2023-10-17 05:26:48 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 05:38:22 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 694.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocOncoTK.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocOncoTK_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocOncoTK.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocOncoTK/DESCRIPTION’ ... OK
* this is package ‘BiocOncoTK’ version ‘1.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
.dockstore.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 7.4Mb
sub-directories of 1Mb or more:
data 2.2Mb
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 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocOncoTK.Rcheck/00check.log’
for details.
BiocOncoTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocOncoTK ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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: 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, aperm, 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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
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")'.
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
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, 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, aperm, 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
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, aperm, 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
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, aperm, 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
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
117.118 7.854 199.925
BiocOncoTK.Rcheck/BiocOncoTK-Ex.timings
| name | user | system | elapsed | |
| CCLE_DRUG_BROAD | 0.122 | 0.005 | 0.169 | |
| MSIsensor.10k | 0.020 | 0.001 | 0.031 | |
| TcgaMutCounts | 0 | 0 | 0 | |
| TcgaNIndWithAnyMut | 0.000 | 0.000 | 0.001 | |
| add_sym | 0 | 0 | 0 | |
| annotTabs | 0.001 | 0.001 | 0.001 | |
| bindMSI | 0.001 | 0.000 | 0.001 | |
| bipg_tests | 0.287 | 0.015 | 0.390 | |
| buildPancanSE | 0.001 | 0.000 | 0.000 | |
| cell_70138 | 0.001 | 0.001 | 0.002 | |
| clueDemos | 0.001 | 0.001 | 0.001 | |
| clueServiceNames | 0 | 0 | 0 | |
| darmGBMcls | 0.321 | 0.011 | 0.436 | |
| dingMSI | 0.002 | 0.001 | 0.004 | |
| featIDMapper | 0.000 | 0.000 | 0.001 | |
| fireMSI | 0.899 | 0.098 | 1.370 | |
| get_plates | 0.001 | 0.000 | 0.002 | |
| ggFeatDens | 0.001 | 0.000 | 0.000 | |
| ggFeatureSegs | 0.001 | 0.001 | 0.001 | |
| ggMutDens | 0.000 | 0.000 | 0.001 | |
| icd10_c | 0.040 | 0.019 | 0.087 | |
| k23sig | 0.003 | 0.001 | 0.004 | |
| loadPatel | 0.001 | 0.000 | 0.000 | |
| mc3toGR | 0.001 | 0.000 | 0.001 | |
| molpo_3utr | 0.114 | 0.005 | 0.146 | |
| molpo_5utr | 0.850 | 0.014 | 1.014 | |
| molpo_CDS | 0.062 | 0.005 | 0.094 | |
| molpo_WGS | 0.014 | 0.001 | 0.026 | |
| oncoPrintISB | 0.000 | 0.001 | 0.000 | |
| pancan.clin.varnames | 0.007 | 0.001 | 0.010 | |
| pancan_BQ | 0.001 | 0.000 | 0.001 | |
| pancan_app | 0 | 0 | 0 | |
| pancan_clinicalTabVarnames | 0 | 0 | 0 | |
| pancan_longname | 0.001 | 0.000 | 0.001 | |
| pancan_sampTypeMap | 0.001 | 0.001 | 0.001 | |
| pancan_tabulate | 0.000 | 0.000 | 0.001 | |
| patient_to_tumor_code | 0.009 | 0.000 | 0.014 | |
| pertClasses | 0 | 0 | 0 | |
| pert_70138 | 0.001 | 0.001 | 0.002 | |
| query_clue | 0.001 | 0.000 | 0.001 | |
| small_msi | 0.005 | 0.001 | 0.008 | |
| tumNorSet | 0.001 | 0.000 | 0.000 | |
| utils | 0.267 | 0.022 | 0.368 | |
| viz_msi_raw | 0 | 0 | 0 | |