Augustin Luna
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/rcellminer |
| git_branch: devel |
| git_last_commit: 48e3a34 |
| git_last_commit_date: 2024-04-30 10:42:38 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:11 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 1641/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rcellminer 2.27.0 (landing page) Augustin Luna
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the rcellminer 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: rcellminer |
| Version: 2.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rcellminer_2.27.0.tar.gz |
| StartedAt: 2024-05-12 23:58:40 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-13 00:00:48 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 128.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rcellminer.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rcellminer_2.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/rcellminer.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘2.27.0’
* 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 ‘rcellminer’ can be installed ... OK
* checking installed package size ... OK
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘shiny’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (7) cmVersion.Rd:17: Invalid email address: vinodh.rajapakse AT nih.gov
checkRd: (-1) drugDB.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:15-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drugDB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (7) drugDB.Rd:45: Invalid email address: vinodh.rajapakse AT nih.gov
checkRd: (-1) elNetMolDataNCI60.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:23-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elNetMolDataNCI60.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (7) elNetMolDataNCI60.Rd:47: Invalid email address: vinodh.rajapakse AT nih.gov
checkRd: (7) fingerprintList.Rd:14: Invalid email address: augustin AT mail.nih.gov
* 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 ... 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/rcellminer.Rcheck/00check.log’
for details.
rcellminer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rcellminer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘rcellminer’ ... ** 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 (rcellminer)
rcellminer.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(rcellminer)
Loading required package: Biobase
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, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
>
> #test_package("rcellminer")
> test_check("rcellminer")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 229 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_getBinaryMutationData.R:1:1'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 229 ]
>
> proc.time()
user system elapsed
60.441 6.458 66.912
rcellminer.Rcheck/rcellminer-Ex.timings
| name | user | system | elapsed | |
| crossCors | 0.786 | 0.040 | 0.830 | |
| crossCorsSpearman | 0 | 0 | 0 | |
| getActivityRangeStats | 0.161 | 0.003 | 0.165 | |
| getColumnQuantiles | 0.003 | 0.001 | 0.002 | |
| getDrugActivityData | 0.034 | 0.001 | 0.035 | |
| getDrugActivityRange | 0.068 | 0.001 | 0.069 | |
| getDrugActivityRepeatData | 0.034 | 0.001 | 0.035 | |
| getDrugMoaList | 0.147 | 0.003 | 0.150 | |
| getDrugName | 0.020 | 0.001 | 0.021 | |
| getFeatureDataFromMatList | 4.406 | 0.201 | 4.629 | |
| getMedSenLineActivity | 0.050 | 0.000 | 0.051 | |
| getMinDrugActivityRepeatCor | 0.316 | 0.011 | 0.328 | |
| getMoaStr | 0.430 | 0.004 | 0.435 | |
| getMoaToCompounds | 0.142 | 0.002 | 0.144 | |
| getMolDataMatrices | 0.386 | 0.023 | 0.409 | |
| getNumDrugActivityRepeats | 0.096 | 0.001 | 0.097 | |
| getNumMissingLines | 0.000 | 0.000 | 0.001 | |
| getRsd | 0.003 | 0.001 | 0.004 | |
| getSmiles | 0.024 | 0.001 | 0.024 | |
| hasMoa | 0.145 | 0.002 | 0.146 | |
| isPublic | 0.001 | 0.001 | 0.002 | |
| loadCellminerPlotInfo | 0.001 | 0.000 | 0.002 | |
| loadNciColorSet | 0.001 | 0.000 | 0.002 | |
| parCorPatternComparison | 0.385 | 0.026 | 0.410 | |
| patternComparison | 0.363 | 0.038 | 0.401 | |
| plotCellMiner | 0.605 | 0.051 | 0.656 | |
| plotCellMiner2D | 0.000 | 0.001 | 0.001 | |
| plotDrugActivityRepeats | 1.146 | 0.062 | 1.209 | |
| plotDrugSets | 0.044 | 0.012 | 0.056 | |
| removeMolDataType | 0.001 | 0.000 | 0.001 | |
| rowCors | 0.001 | 0.000 | 0.001 | |
| searchForNscs | 0.054 | 0.003 | 0.058 | |
| selectCorrelatedRows | 0.001 | 0.001 | 0.002 | |
| selectCorrelatedRowsFromMatrices | 0.003 | 0.002 | 0.004 | |