Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:07:59 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for CoreGx on merida1


To the developers/maintainers of the CoreGx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoreGx.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 413/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoreGx 2.0.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_15
git_last_commit: 6b5b262
git_last_commit_date: 2022-04-26 12:05:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CoreGx
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoreGx_2.0.0.tar.gz
StartedAt: 2022-05-18 00:51:54 -0400 (Wed, 18 May 2022)
EndedAt: 2022-05-18 00:58:52 -0400 (Wed, 18 May 2022)
EllapsedTime: 417.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoreGx_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoreGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoreGx’ version ‘2.0.0’
* 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 ‘CoreGx’ 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 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
Found the following possibly unsafe calls:
File ‘CoreGx/R/updateObject-methods.R’:
  unlockBinding("colIDs", getIntern(treatmentResponse))

.checkForIdColumn: no visible binding for global variable ‘col_col’
.compareSensitivityInfo: no visible binding for global variable
  ‘drugid’
.compareSensitivityInfo: no visible binding for global variable
  ‘cellid’
.rebuildInfo: no visible global function definition for ‘patterns’
.rebuildInfo: no visible binding for global variable ‘..keepCols’
.rebuildInfo: no visible binding for global variable ‘replicate_id’
.rebuildInfo: no visible binding for global variable ‘drug1id’
.rebuildInfo: no visible binding for global variable ‘cellid’
.rebuildInfo: no visible binding for global variable ‘drugid’
.rebuildInfo: no visible binding for global variable ‘drug_uid’
.rebuildInfo: no visible binding for global variable ‘..rowIDcols’
.rebuildInfo: no visible binding for global variable ‘sample_uid’
.rebuildInfo: no visible binding for global variable ‘..colIDcols’
.rebuildInfo: no visible binding for global variable ‘exp_id’
.rebuildProfiles: no visible binding for global variable ‘sample_uid’
.rebuildProfiles: no visible binding for global variable ‘drug_uid’
.rebuildProfiles: no visible binding for global variable ‘exp_id’
.rebuildRaw: no visible binding for global variable ‘.NATURAL’
.rebuildRaw: no visible binding for global variable ‘sampleid’
.rebuildRaw: no visible binding for global variable ‘exp_id’
.rebuildRaw: no visible binding for global variable ‘drug1id’
.rebuildRaw: no visible binding for global variable ‘row_ids’
.rebuildRaw: no visible binding for global variable ‘col_ids’
.rebuildRaw: no visible binding for global variable ‘dose’
.rebuildRaw: no visible global function definition for ‘patterns’
.rebuildSensNumber: no visible global function definition for
  ‘patterns’
.rebuildSensNumber: no visible binding for global variable ‘.drugCombo’
.rebuildSensNumber: no visible binding for global variable
  ‘.sampleCombo’
.sensitivityToTRE: no visible binding for global variable ‘dose’
.sensitivityToTRE: no visible binding for global variable ‘viability’
.sensitivityToTRE: no visible binding for global variable
  ‘replicate_id’
.sensitivityToTRE: no visible binding for global variable ‘rn’
.sensitivityToTRE: no visible binding for global variable ‘drugid’
.sensitivityToTRE: no visible binding for global variable ‘cellid’
CoreSet: no visible binding for global variable ‘cell’
CoreSet: no visible binding for global variable ‘drug’
CoreSet: no visible global function definition for ‘.checkForIdColumns’
assay<-,LongTable-character: no visible binding for global variable
  ‘..missingRowCols’
assay<-,LongTable-character: no visible binding for global variable
  ‘..missingColCols’
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable ‘.sample’
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable ‘.feature’
colData<-,LongTable-ANY: no visible binding for global variable
  ‘.NATURAL’
colData<-,LongTable-ANY: no visible binding for global variable
  ‘.colnames’
metaConstruct,LongTableDataMapper: no visible binding for global
  variable ‘..rowIDs’
metaConstruct,LongTableDataMapper: no visible binding for global
  variable ‘..colIDs’
rowData<-,LongTable: no visible binding for global variable ‘.NATURAL’
rowData<-,LongTable: no visible binding for global variable ‘.rownames’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘V2’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘V1’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘sample_uid’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘rn’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘row_id’
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  ‘col_id’
sensitivitySlot<-,CoreSet-list_OR_LongTable: no visible binding for
  global variable ‘funContext’
updateObject,CoreSet: no visible global function definition for
  ‘isValid’
Undefined global functions or variables:
  ..colIDcols ..colIDs ..keepCols ..missingColCols ..missingRowCols
  ..rowIDcols ..rowIDs .NATURAL .checkForIdColumns .colnames .drugCombo
  .feature .rownames .sample .sampleCombo V1 V2 cell cellid col_col
  col_id col_ids dose drug drug1id drug_uid drugid exp_id funContext
  isValid patterns replicate_id rn row_id row_ids sample_uid sampleid
  viability
* 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 8 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck/00check.log’
for details.



Installation output

CoreGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoreGx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘CoreGx’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘CoreGx’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘CoreGx’
** 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 (CoreGx)

Tests output

CoreGx.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(CoreGx)
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: 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: S4Vectors

Attaching package: 'S4Vectors'

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

> 
> test_check("CoreGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 17.341   0.757  18.110 

Example timings

CoreGx.Rcheck/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors1.9480.0822.031
CoreSet-utils1.4700.0081.480
CoreSet0.0220.0030.025
CoreSet20.0230.0030.027
LongTable-accessors0.0020.0030.004
LongTable-class0.4990.0220.521
LongTable0.0170.0030.019
LongTableDataMapper-accessors0.0050.0000.005
LongTableDataMapper-class0.0090.0000.009
LongTableDataMapper0.0090.0030.012
amcc1.7080.2184.001
as2.5060.9071.240
as.long.table0.2500.0280.277
assayCols0.0000.0010.000
buildLongTable-list-method0.0000.0000.001
buildLongTable000
callingWaterfall000
cash-LongTable-method0.0150.0020.017
cash-set-LongTable-method0.0650.0050.069
checkColumnCardinality0.0030.0000.004
checkCsetStructure0.0480.0040.052
colIDs0.0000.0000.001
colMeta000
connectivityScore0.2130.2120.398
cosinePerm0.1690.2080.349
dot-0.0010.0000.001
dot-distancePointLine0.0000.0010.001
dot-distancePointSegment0.0010.0010.002
dot-intersectList0.0000.0010.001
dot-symSetDiffList0.0010.0010.002
dot-unionList0.0000.0000.001
getIntern0.0010.0000.001
guessMapping-LongTableDataMapper-method0.0140.0030.016
gwc0.2270.2070.407
idCols-LongTable-method0.0010.0010.001
idCols000
is.items0.0000.0000.001
mcc0.0240.0564.261
metaConstruct3.8580.6810.279
reindex000
rowIDs0.0010.0000.000
rowMeta0.0000.0000.001
sensitivityInfo-set000
sensitivityInfo0.0000.0000.001
sensitivityMeasures-set000
sensitivityMeasures0.0180.0020.020
sensitivityProfiles0.0000.0000.001
sensitivityRaw0.0000.0000.001
sensitivitySlotToLongTable0.0010.0000.000
show-CoreSet-method0.0130.0020.016
show-LongTable-method0.0130.0020.015
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.5820.0750.659
sub-subset-LongTable-ANY-ANY-method0.0580.0060.064
subset-LongTable-method0.3840.0350.419
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateSampleId0.2810.0280.309
updateTreatmentId0.0130.0020.015