Multiple platform build/check report for BioC 3.19 - CHECK results for CoreGx on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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*

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### Running command:
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###   /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_2.7.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CoreGx.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoreGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoreGx’ version ‘2.7.3’
* 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 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.LongTable’ ‘.parseToRoxygen’ ‘.sensitivityToTRE’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.meshEval2: no visible binding for global variable ‘n’
.meshEval2: no visible binding for global variable ‘family’
.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 ‘treatment1id’
.rebuildInfo: no visible binding for global variable ‘sampleid’
.rebuildInfo: no visible binding for global variable ‘treatmentid’
.rebuildInfo: no visible binding for global variable ‘treatment_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
  ‘treatment_uid’
.rebuildProfiles: no visible binding for global variable ‘sample_uid’
.rebuildProfiles: no visible binding for global variable ‘exp_id’
.rebuildProfiles: no visible binding for global variable ‘N’
.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 ‘treatment1id’
.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
  ‘.treatmentCombo’
.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 ‘treatmentid’
.sensitivityToTRE: no visible binding for global variable ‘sampleid’
.update_dimData: no visible binding for global variable ‘N’
.update_dimData: no visible binding for global variable ‘.NATURAL’
.update_dimData: no visible binding for global variable ‘.rownames’
CoreSet: no visible binding for global variable ‘cell’
CoreSet: no visible binding for global variable ‘drug’
aggregate2: no visible binding for global variable ‘group_id’
aggregate2: no visible binding for global variable ‘split_id’
cardinality: no visible binding for global variable ‘N’
checkColumnCardinality: no visible binding for global variable ‘N’
optimizeCoreGx: no visible binding for global variable ‘nthread’
optimizeCoreGx: no visible binding for global variable ‘total_time’
optimizeCoreGx: no visible binding for global variable ‘mem_alloc’
optimizeCoreGx: no visible binding for global variable ‘itr/sec’
optimizeCoreGx: no visible binding for global variable ‘gc/sec’
optimizeCoreGx: no visible binding for global variable ‘median_sec’
optimizeCoreGx: no visible binding for global variable ‘N’
buildComboProfiles,LongTable: no visible binding for global variable
  ‘treatment2dose’
buildComboProfiles,LongTable: no visible binding for global variable
  ‘treatment1dose’
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable ‘.sample’
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable ‘.feature’
reindex,LongTable: no visible binding for global variable ‘.rowKey’
reindex,LongTable: no visible binding for global variable ‘.colKey’
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
  ‘rn’
treatmentResponse<-,CoreSet-list_OR_LongTable: no visible binding for
  global variable ‘funContext’
updateObject,CoreSet: no visible global function definition for
  ‘isValid’
updateObject,LongTable: no visible global function definition for
  ‘isValid’
Undefined global functions or variables:
  ..colIDcols ..keepCols ..rowIDcols .NATURAL .colKey .feature .rowKey
  .rownames .sample .sampleCombo .treatmentCombo N V1 V2 cell dose drug
  exp_id family funContext gc/sec group_id isValid itr/sec median_sec
  mem_alloc n nthread patterns replicate_id rn sample_uid sampleid
  split_id total_time treatment1dose treatment1id treatment2dose
  treatment_uid treatmentid viability
Consider adding
  importFrom("stats", "family")
to your NAMESPACE file.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'LongTable-class.Rd':
  ‘`x`’ ‘`i`’

Documented arguments not in \usage in Rd file 'assays-LongTableDataMapper-method.Rd':
  ‘withDimNames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'setOps-immutable.Rd':
  ‘subset.immutable’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 99 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
metaConstruct 8.960  0.740   7.514
as            4.676  0.705   4.309
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/CoreGx.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoreGx
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘CoreGx’ ...
** 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 (CoreGx)

Tests output


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(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, 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

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 object is masked from 'package:utils':

    findMatches

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")

Attaching package: 'data.table'

The following object is masked from 'package:SummarizedExperiment':

    shift

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-LongTable-accessors.R:13:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
181.346   3.435 186.579

Example timings

name	user	system	elapsed
CoreSet-accessors	1.879	0.046	1.932
CoreSet-utils	0.392	0.032	0.428
CoreSet	0.043	0.004	0.048
CoreSet2	0.018	0.003	0.021
LongTable-accessors	0.001	0.001	0.002
LongTable-class	0.564	0.040	0.609
LongTable	0.000	0.001	0.000
LongTableDataMapper-accessors	0.003	0.001	0.004
LongTableDataMapper-class	0.007	0.000	0.007
LongTableDataMapper	0.007	0.002	0.009
TREDataMapper-accessors	0.098	0.002	0.100
amcc	3.005	0.152	4.225
as	4.676	0.705	4.309
as.long.table	3.495	0.037	3.552
assayCols	0	0	0
assayIndex	0	0	0
assayKeys	0	0	0
assignment-immutable	0.002	0.000	0.002
buildComboProfiles-LongTable-method	0.000	0.000	0.001
buildComboProfiles	0	0	0
buildLongTable-list-method	0	0	0
buildLongTable	0	0	0
callingWaterfall	0	0	0
cash-LongTable-method	0.010	0.001	0.012
cash-set-LongTable-method	0.060	0.001	0.061
checkColumnCardinality	0.004	0.000	0.003
checkCsetStructure	0.032	0.002	0.033
colIDs	0.000	0.000	0.001
colMeta	0	0	0
connectivityScore	0.083	0.091	0.167
cosinePerm	0.058	0.094	0.143
dot-	0.000	0.002	0.002
dot-distancePointLine	0	0	0
dot-distancePointSegment	0.000	0.004	0.004
dot-fitCurve2	0	0	0
dot-intersectList	0.001	0.002	0.002
dot-symSetDiffList	0.001	0.001	0.001
dot-unionList	0.001	0.000	0.000
endoaggregate	0.000	0.001	0.002
getIntern-set	0	0	0
getIntern	0.000	0.001	0.000
guessMapping-LongTableDataMapper-method	0.013	0.012	0.025
guessMapping	0.000	0.001	0.000
gwc	0.108	0.088	0.186
idCols	0.000	0.003	0.003
immutable	0.003	0.022	0.026
is.items	0.001	0.002	0.002
mcc	0.015	0.021	2.256
mergeAssays	0.000	0.001	0.000
metaConstruct	8.960	0.740	7.514
mutable	0.000	0.000	0.001
optimizeCoreGx	0.000	0.000	0.001
reindex	0.000	0.001	0.000
rowIDs	0	0	0
rowMeta	0	0	0
sensitivityInfo-set	0.000	0.000	0.001
sensitivityInfo	0.000	0.000	0.001
sensitivityMeasures-set	0.000	0.000	0.001
sensitivityMeasures	0.015	0.001	0.016
sensitivityProfiles	0	0	0
sensitivityRaw	0	0	0
sensitivitySlotToLongTable	0.000	0.001	0.001
setOps-immutable	0.000	0.000	0.001
show-CoreSet-method	0.012	0.001	0.014
show-LongTable-method	0.006	0.000	0.007
showSigAnnot	0	0	0
sub-LongTable-ANY-ANY-ANY-method	0.315	0.012	0.330
sub-subset-LongTable-ANY-ANY-method	0.060	0.003	0.064
subset-LongTable-method	0.153	0.008	0.162
subsetTo	0.000	0.001	0.000
summarizeMolecularProfiles	0.000	0.000	0.001
summarizeSensitivityProfiles	0.001	0.000	0.000
updateSampleId	0.158	0.008	0.167
updateTreatmentId	0.011	0.002	0.013

CHECK results for CoreGx on lconway

Summary

Command output

Installation output

Tests output

Example timings