Karim Mezhoud
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/bioCancer |
| git_branch: RELEASE_3_18 |
| git_last_commit: 94d43a0 |
| git_last_commit_date: 2024-02-14 15:48:31 -0400 (Wed, 14 Feb 2024) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 170/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bioCancer 1.30.8 (landing page) Karim Mezhoud
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the bioCancer 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: bioCancer |
| Version: 1.30.8 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.30.8.tar.gz |
| StartedAt: 2024-04-17 06:57:08 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 07:04:33 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 445.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioCancer.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.30.8.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/bioCancer.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.30.8’
* 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 ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
app 3.3Mb
extdata 1.7Mb
* 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
checkDimensions : <anonymous>: no visible global function definition
for ‘pull’
getList_Cases : <anonymous>: no visible global function definition for
‘pull’
getList_GenProfs : <anonymous>: no visible global function definition
for ‘pull’
Undefined global functions or variables:
pull
* 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 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/bioCancer.Rcheck/00check.log’
for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘bioCancer’ ... ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
> library(testthat)
> library(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: ggplot2
Loading required package: lubridate
Attaching package: 'lubridate'
The following objects are masked from 'package:base':
date, intersect, setdiff, union
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
The following object is masked from 'package:testthat':
matches
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'radiant.data'
The following objects are masked from 'package:lubridate':
month, wday
The following object is masked from 'package:ggplot2':
diamonds
The following object is masked from 'package:magrittr':
set_attr
The following object is masked from 'package:testthat':
describe
The following object is masked from 'package:base':
date
Loading required package: cBioPortalData
Loading required package: AnVIL
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:dplyr':
count
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 object is masked from 'package:radiant.data':
normalize
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:lubridate':
intersect, setdiff, union
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 objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:tidyr':
expand
The following objects are masked from 'package:lubridate':
second, second<-
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
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
The following object is masked from 'package:lubridate':
%within%
Loading required package: GenomeInfoDb
Attaching package: 'GenomicRanges'
The following object is masked from 'package:magrittr':
subtract
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: XML
>
> test_check("bioCancer")
getCancerStudies... OK
getCaseLists (1/1) ... OK
getClinicalData (1/1) ... OK
getGeneticProfiles (1/1) ... OK
getProfileData (1/1) ... OK
ReactomeFI connection... OK
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_funs.R:8:1', 'test_funs.R:20:1'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
>
> proc.time()
user system elapsed
22.620 1.202 25.401
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| AnnotationFuncs | 0.222 | 0.011 | 0.236 | |
| Edges_Diseases_obj | 0.003 | 0.001 | 0.003 | |
| Mutation_obj | 0.115 | 0.013 | 0.473 | |
| Node_Diseases_obj | 0.001 | 0.000 | 0.001 | |
| Node_df_FreqIn | 0 | 0 | 0 | |
| Node_obj_CNA_ProfData | 0.030 | 0.002 | 0.133 | |
| Node_obj_FreqIn | 0.000 | 0.000 | 0.001 | |
| Node_obj_Met_ProfData | 0.026 | 0.004 | 0.128 | |
| Node_obj_mRNA_Classifier | 0.001 | 0.000 | 0.000 | |
| Studies_obj | 0.003 | 0.000 | 0.004 | |
| UnifyRowNames | 0.027 | 0.006 | 0.142 | |
| attriColorGene | 0.087 | 0.007 | 0.202 | |
| attriColorValue | 0.030 | 0.003 | 0.165 | |
| attriColorVector | 0.033 | 0.002 | 0.137 | |
| attriShape2Gene | 0 | 0 | 0 | |
| attriShape2Node | 0.001 | 0.000 | 0.000 | |
| bioCancer | 0 | 0 | 0 | |
| checkDimensions | 0.052 | 0.002 | 0.154 | |
| coffeewheel | 0.000 | 0.001 | 0.000 | |
| coffeewheelOutput | 0 | 0 | 0 | |
| displayTable | 0.062 | 0.003 | 0.165 | |
| findPhantom | 0.000 | 0.000 | 0.001 | |
| getEvidenceCodes | 0.000 | 0.000 | 0.001 | |
| getFreqMutData | 0.064 | 0.003 | 0.184 | |
| getGenesClassification | 0.063 | 0.003 | 0.165 | |
| getListProfData | 0.062 | 0.003 | 0.165 | |
| getList_Cases | 0.062 | 0.003 | 0.166 | |
| getList_GenProfs | 0.215 | 0.004 | 0.321 | |
| getOrthologs | 0 | 0 | 0 | |
| getProfData | 0.062 | 0.002 | 0.165 | |
| getSequensed_SampleSize | 0 | 0 | 0 | |
| mapLists | 0.000 | 0.001 | 0.001 | |
| metabologram | 0.000 | 0.000 | 0.001 | |
| metabologramOutput | 0.000 | 0.000 | 0.001 | |
| pickGO | 0.115 | 0.006 | 0.127 | |
| pickRefSeq | 0.067 | 0.004 | 0.073 | |
| reStrColorGene | 0.063 | 0.003 | 0.167 | |
| reStrDimension | 0.063 | 0.003 | 0.164 | |
| reStrDisease | 0.062 | 0.002 | 0.162 | |
| removeNAs | 0.001 | 0.000 | 0.000 | |
| renderCoffeewheel | 0 | 0 | 0 | |
| renderMetabologram | 0.000 | 0.001 | 0.000 | |
| returnTextAreaInput | 0 | 0 | 0 | |
| translate | 0.123 | 0.006 | 0.128 | |
| whichGeneList | 0 | 0 | 0 | |
| widgetThumbnail | 0 | 0 | 0 | |