Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-07-01 12:05:09 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 2.0.2  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_15
git_last_commit: 4bceca0
git_last_commit_date: 2022-05-20 15:47:01 -0400 (Fri, 20 May 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: 2.0.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CoreGx_2.0.2.tar.gz
StartedAt: 2022-06-30 19:22:13 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 19:28:14 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 360.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CoreGx_2.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.2’
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.LongTable’ ‘.sensitivityToTRE’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  subset.immutable
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkForIdColumn: no visible binding for global variable ‘col_col’
.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 ‘sample_uid’
.rebuildProfiles: no visible binding for global variable
  ‘treatment_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 ‘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’
CoreSet: no visible binding for global variable ‘cell’
CoreSet: no visible binding for global variable ‘drug’
CoreSet: no visible global function definition for ‘.checkForIdColumns’
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’
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’
reindex,LongTable: no visible binding for global variable ‘.rowKey’
reindex,LongTable: no visible binding for global variable ‘.colKey’
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’
updateObject,LongTable: no visible global function definition for
  ‘isValid’
Undefined global functions or variables:
  ..colIDcols ..keepCols ..rowIDcols .NATURAL .checkForIdColumns
  .colKey .colnames .feature .rowKey .rownames .sample .sampleCombo
  .treatmentCombo N V1 V2 cell col_col col_id col_ids dose drug exp_id
  funContext gc/sec isValid itr/sec median_sec mem_alloc nthread
  patterns replicate_id rn row_id row_ids sample_uid sampleid
  total_time treatment1id treatment_uid treatmentid 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 ... 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 8 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
optimizeCoreGx 192.331   1.78 141.035
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck/00check.log’
for details.



Installation output

CoreGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CoreGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  9.857   0.520  10.362 

Example timings

CoreGx.Rcheck/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors0.9920.0671.028
CoreSet-utils0.4980.0010.498
CoreSet0.0110.0040.015
CoreSet20.0150.0010.015
LongTable-accessors0.0020.0000.001
LongTable-class1.2660.1031.160
LongTable0.0010.0000.000
LongTableDataMapper-accessors0.0000.0040.004
LongTableDataMapper-class0.0050.0000.005
LongTableDataMapper0.0050.0000.005
amcc1.6650.1322.592
as1.2650.7320.905
as.long.table0.1890.0110.122
assayCols0.0010.0000.000
assignment-immutable0.0020.0010.002
buildLongTable-list-method000
buildLongTable000
callingWaterfall0.0000.0000.001
cash-LongTable-method0.0200.0030.014
cash-set-LongTable-method0.0780.0160.057
checkColumnCardinality0.0040.0000.003
checkCsetStructure0.0240.0000.021
colIDs0.0000.0000.001
colMeta0.0000.0000.001
connectivityScore0.0130.0120.124
cosinePerm0.0960.0610.122
dot-0.0000.0010.001
dot-distancePointLine0.0000.0010.001
dot-distancePointSegment0.0000.0010.001
dot-intersectList000
dot-symSetDiffList0.0000.0000.001
dot-unionList0.0000.0000.001
getIntern-set0.0000.0010.001
getIntern0.0000.0010.001
guessMapping-LongTableDataMapper-method0.0710.0510.009
guessMapping000
gwc0.0330.0130.203
idCols-LongTable-method0.0000.0010.002
idCols0.0000.0010.001
immutable0.0020.0010.002
is.immutable000
is.items0.0000.0000.001
mcc0.1100.1171.678
metaConstruct1.5000.3380.120
optimizeCoreGx192.331 1.780141.035
reindex000
rowIDs000
rowMeta000
sensitivityInfo-set0.0010.0000.001
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures0.0090.0000.009
sensitivityProfiles000
sensitivityRaw000
sensitivitySlotToLongTable000
setOps-immutable0.0010.0000.000
show-CoreSet-method0.0060.0000.006
show-LongTable-method0.0060.0000.006
showSigAnnot0.0010.0000.000
sub-LongTable-ANY-ANY-ANY-method1.0500.0040.981
sub-subset-LongTable-ANY-ANY-method0.0600.0000.032
subset-LongTable-method0.2420.0000.150
subsetTo000
summarizeMolecularProfiles000
summarizeSensitivityProfiles0.0000.0010.001
updateSampleId0.1430.0030.138
updateTreatmentId0.0030.0040.006