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This page was generated on 2021-09-22 15:05:40 -0400 (Wed, 22 Sep 2021).

CHECK results for CoreGx on machv2

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? here 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 393/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoreGx 1.4.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_13
git_last_commit: 1bc1d98
git_last_commit_date: 2021-05-31 16:11:19 -0400 (Mon, 31 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CoreGx
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoreGx_1.4.1.tar.gz
StartedAt: 2021-09-21 17:54:14 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 17:59:12 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 298.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoreGx_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CoreGx.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.4.1’
* 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
.rebuildInfo: no visible global function definition for ‘patterns’
.rebuildInfo: no visible binding for global variable ‘..keepCols’
.rebuildInfo: no visible binding for global variable ‘drugid’
.rebuildInfo: no visible binding for global variable ‘..rowIDcols’
.rebuildInfo: no visible binding for global variable ‘cellid’
.rebuildInfo: no visible binding for global variable ‘..colIDcols’
.rebuildInfo: no visible binding for global variable ‘exp_id’
.rebuildRaw: no visible binding for global variable ‘.NATURAL’
.rebuildRaw: no visible binding for global variable ‘row_ids’
.rebuildRaw: no visible binding for global variable ‘col_ids’
.rebuildRaw : .paste_slashes: no visible binding for global variable
  ‘..’
.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 ‘.cellCombo’
.sensitivityToLongTable: no visible binding for global variable
  ‘replicate_id’
colData<-,LongTable-ANY: no visible binding for global variable
  ‘.NATURAL’
colData<-,LongTable-ANY: no visible binding for global variable
  ‘.colnames’
colData<-,LongTable-ANY: no visible binding for global variable
  ‘..colIDcols’
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’
rowData<-,LongTable: no visible binding for global variable
  ‘..rowIDCols’
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’
Undefined global functions or variables:
  .. ..colIDcols ..colIDs ..keepCols ..rowIDCols ..rowIDcols ..rowIDs
  .NATURAL .cellCombo .colnames .drugCombo .rownames cellid col_id
  col_ids dose drugid exp_id funContext patterns replicate_id rn row_id
  row_ids
* 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-3.13-bioc/meat/CoreGx.Rcheck/00check.log’
for details.



Installation output

CoreGx.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CoreGx’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'ggplot2':
  method        from
  print.element sets
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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 
 11.204   0.574  11.771 

Example timings

CoreGx.Rcheck/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors2.3290.1642.496
Create0.0700.0040.074
LongTable-class0.4940.0270.521
LongTableDataMapper-accessors0.0030.0010.003
LongTableDataMapper-class0.0030.0010.004
amcc2.0220.0682.095
as0.1430.0050.148
as.data.frame.LongTable0.2890.4130.703
as.long.table0.0540.0010.055
assayCols0.0000.0000.001
buildLongTable0.0000.0010.000
callingWaterfall000
cash-LongTable-method0.0110.0020.014
cash-set-LongTable-method0.0720.0040.076
checkColumnCardinality0.0030.0010.003
checkCsetStructure0.0710.0010.071
colIDs000
colMeta000
connectivityScore0.0810.0030.084
cosinePerm0.0530.0020.055
dot-000
dot-distancePointLine0.0010.0010.000
dot-distancePointSegment0.0000.0010.001
dot-intersectList0.0010.0010.000
dot-symSetDiffList0.0010.0000.000
dot-unionList0.0010.0000.001
getIntern0.0010.0010.001
guessMapping-LongTableDataMapper-method0.0110.0010.011
gwc0.1110.0050.115
idCols-LongTable-method0.0000.0000.001
idCols000
is.items0.0010.0010.000
mcc2.5820.0562.640
metaConstruct0.1030.0030.106
reindex0.0010.0010.000
rowIDs000
rowMeta000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set0.0010.0010.000
sensitivityMeasures0.0050.0000.006
sensitivityProfiles0.0000.0000.001
sensitivityRaw000
sensitivitySlotToLongTable0.0010.0000.000
show-CoreSet-method0.0350.0010.036
show-LongTable-method0.0080.0000.008
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.4630.0060.468
sub-subset-LongTable-ANY-ANY-method0.0900.0050.095
subset-LongTable-method0.2950.0040.299
summarizeMolecularProfiles000
summarizeSensitivityProfiles0.0000.0010.000
updateCellId0.4030.0030.407