Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-30 11:36:29 -0500 (Thu, 30 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4685
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4420
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4439
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 436/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoreGx 2.6.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2023-11-29 14:05:05 -0500 (Wed, 29 Nov 2023)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_18
git_last_commit: ba1a202
git_last_commit_date: 2023-10-24 11:22:13 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for CoreGx on palomino4


To the developers/maintainers of the CoreGx package:
- 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 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: CoreGx
Version: 2.6.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CoreGx_2.6.0.tar.gz
StartedAt: 2023-11-30 00:31:54 -0500 (Thu, 30 Nov 2023)
EndedAt: 2023-11-30 00:38:20 -0500 (Thu, 30 Nov 2023)
EllapsedTime: 386.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CoreGx_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/CoreGx.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '2.6.0'
* 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 '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 ... 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 '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
  '.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 col_ids
  dose drug exp_id family funContext gc/sec group_id isValid itr/sec
  median_sec mem_alloc n nthread patterns replicate_id rn row_ids
  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
S3 methods shown with full name in documentation object 'setOps-immutable':
  '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
amcc              2.80   0.06   26.15
gwc               0.82   0.00   11.72
mcc               0.68   0.02   13.02
cosinePerm        0.69   0.00   10.78
connectivityScore 0.67   0.00   10.98
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/CoreGx.Rcheck/00check.log'
for details.



Installation output

CoreGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL CoreGx
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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

CoreGx.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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, 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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 
  41.64    1.50   81.60 

Example timings

CoreGx.Rcheck/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors1.830.071.95
CoreSet-utils0.330.000.33
CoreSet0.070.000.06
CoreSet20.010.000.01
LongTable-accessors0.020.000.02
LongTable-class1.150.031.20
LongTable000
LongTableDataMapper-accessors0.020.000.02
LongTableDataMapper-class000
LongTableDataMapper0.000.020.01
TREDataMapper-accessors0.060.000.07
amcc 2.80 0.0626.15
as0.290.000.33
as.long.table0.110.000.10
assayCols000
assayIndex000
assayKeys000
assignment-immutable000
buildComboProfiles-LongTable-method000
buildComboProfiles000
buildLongTable-list-method000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.020.000.02
cash-set-LongTable-method0.060.000.06
checkColumnCardinality0.010.000.01
checkCsetStructure0.020.000.02
colIDs000
colMeta000
connectivityScore 0.67 0.0010.98
cosinePerm 0.69 0.0010.78
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-fitCurve2000
dot-intersectList000
dot-symSetDiffList000
dot-unionList000
endoaggregate000
getIntern-set000
getIntern000
guessMapping-LongTableDataMapper-method0.010.000.01
guessMapping000
gwc 0.82 0.0011.72
idCols000
immutable000
is.items000
mcc 0.68 0.0213.02
mergeAssays000
metaConstruct0.070.020.08
mutable000
optimizeCoreGx000
reindex000
rowIDs000
rowMeta000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures0.020.000.02
sensitivityProfiles000
sensitivityRaw000
sensitivitySlotToLongTable000
setOps-immutable000
show-CoreSet-method0.010.000.01
show-LongTable-method000
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.240.030.27
sub-subset-LongTable-ANY-ANY-method0.060.000.06
subset-LongTable-method0.110.030.15
subsetTo000
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateSampleId0.140.000.14
updateTreatmentId000