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This page was generated on 2024-03-27 11:38:31 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 1668/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 2.25.0  (landing page)
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/rcellminer
git_branch: devel
git_last_commit: d55707b
git_last_commit_date: 2023-10-24 10:42:26 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for rcellminer on palomino3


To the developers/maintainers of the rcellminer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rcellminer.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: rcellminer
Version: 2.25.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rcellminer.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings rcellminer_2.25.0.tar.gz
StartedAt: 2024-03-27 05:29:12 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 05:31:39 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 146.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rcellminer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rcellminer.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings rcellminer_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/rcellminer.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rcellminer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rcellminer' version '2.25.0'
* 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/rcellminer.Rcheck/00check.log'
for details.


Installation output

rcellminer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL rcellminer
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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)

Tests output

rcellminer.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 228 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_getBinaryMutationData.R:1:1'

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 228 ]
> 
> proc.time()
   user  system elapsed 
  65.39    8.57   74.01 

Example timings

rcellminer.Rcheck/rcellminer-Ex.timings

nameusersystemelapsed
crossCors0.490.091.04
crossCorsSpearman000
getActivityRangeStats0.200.010.22
getColumnQuantiles0.020.000.02
getDrugActivityData0.040.000.05
getDrugActivityRange0.100.000.09
getDrugActivityRepeatData0.040.000.05
getDrugMoaList0.140.000.14
getDrugName0.020.000.02
getFeatureDataFromMatList3.470.414.67
getMedSenLineActivity0.050.000.05
getMinDrugActivityRepeatCor0.350.030.38
getMoaStr0.250.000.25
getMoaToCompounds0.090.000.09
getMolDataMatrices0.390.030.42
getNumDrugActivityRepeats0.080.000.08
getNumMissingLines0.000.010.02
getRsd000
getSmiles0.030.000.03
hasMoa0.160.000.15
isPublic000
loadCellminerPlotInfo000
loadNciColorSet0.000.020.02
parCorPatternComparison0.450.050.50
patternComparison0.370.030.41
plotCellMiner0.450.120.58
plotCellMiner2D000
plotDrugActivityRepeats1.020.181.33
plotDrugSets0.250.090.35
removeMolDataType000
rowCors000
searchForNscs0.040.000.04
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices000