Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-11-27 14:04:57 -0500 (Sat, 27 Nov 2021).

CHECK results for CoreGx on riesling1

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 398/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoreGx 1.7.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: master
git_last_commit: b78b5a5
git_last_commit_date: 2021-10-26 12:59:39 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'piano' which is not available

Summary

Package: CoreGx
Version: 1.7.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoreGx_1.7.0.tar.gz
StartedAt: 2021-11-27 01:12:59 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 01:18:19 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 319.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoreGx_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '1.7.0'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.paste_slashes: no visible binding for global variable '..'
.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 'drug1id'
.rebuildInfo: no visible binding for global variable 'drug_uid'
.rebuildInfo: no visible binding for global variable '..rowIDcols'
.rebuildInfo: no visible binding for global variable 'cell_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 'cell_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 'cellid'
.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 '.cellCombo'
.sensitivityToLongTable: no visible binding for global variable 'dose'
.sensitivityToLongTable: no visible binding for global variable
  'viability'
.sensitivityToLongTable: no visible binding for global variable
  'replicate_id'
.summarizePerturbationNumbers: no visible global function definition
  for 'drugInfo'
.summarizeSensitivityNumbers: no visible global function definition for
  'drugInfo'
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
  'cell_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 .cellCombo .colnames .drugCombo
  .feature .rownames .sample V1 V2 cell_uid cellid col_id col_ids dose
  drug1id drugInfo drug_uid drugid exp_id funContext isValid patterns
  replicate_id rn row_id row_ids 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
amcc              1.34   0.03   15.42
connectivityScore 0.47   0.00    7.05
gwc               0.44   0.03    7.72
cosinePerm        0.43   0.00    6.98
mcc               0.43   0.00    8.42
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck/00check.log'
for details.



Installation output

CoreGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/CoreGx_1.7.0.tar.gz && rm -rf CoreGx.buildbin-libdir && mkdir CoreGx.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoreGx.buildbin-libdir CoreGx_1.7.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CoreGx_1.7.0.zip && rm CoreGx_1.7.0.tar.gz CoreGx_1.7.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1215k    0  1137    0     0   6423      0  0:03:13 --:--:--  0:03:13  6387
100 1215k  100 1215k    0     0  2401k      0 --:--:-- --:--:-- --:--:-- 2396k
only one architecture so ignoring '--merge-multiarch'
* 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
  converting help for package 'CoreGx'
    finding HTML links ... done
    CoreSet-accessors                       html  
    CoreSet-class                           html  
    CoreSet-utils                           html  
    CoreSet                                 html  
    CoreSet2                                html  
    Create                                  html  
    DataMapper-accessors                    html  
    DataMapper-class                        html  
    LongTable-accessors                     html  
    LongTable-class                         html  
    LongTable                               html  
    LongTableDataMapper-accessors           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/CoreGx.buildbin-libdir/00LOCK-CoreGx/00new/CoreGx/help/assayMap+2CLongTableDataMapper+2CList-method.html
    LongTableDataMapper-class               html  
    LongTableDataMapper                     html  
    TREDataMapper-class                     html  
    TREDataMapper                           html  
    TreatmentResponseExperiment-class       html  
    TreatmentResponseExperiment             html  
    amcc                                    html  
    as                                      html  
    as.long.table                           html  
    assayCols                               html  
    buildLongTable                          html  
    callingWaterfall                        html  
    cash-LongTable-method                   html  
    cash-set-LongTable-method               html  
    checkColumnCardinality                  html  
    checkCsetStructure                      html  
    clevelandSmall_cSet                     html  
    colIDs                                  html  
    colMeta                                 html  
    connectivityScore                       html  
    cosinePerm                              html  
    dot-                                    html  
    dot-assayToBumpyMatrix                  html  
    dot-convertCSetMolecularProfilesToSE    html  
    dot-distancePointLine                   html  
    dot-distancePointSegment                html  
    dot-intersectList                       html  
    dot-longTableToSummarizedExperiment     html  
    dot-sensitivityToLongTable              html  
    dot-symSetDiffList                      html  
    dot-unionList                           html  
    drugSensitivitySig                      html  
    exampleDataMapper                       html  
    getIntern                               html  
    guessMapping-LongTableDataMapper-method
                                            html  
    guessMapping                            html  
    gwc                                     html  
    idCols-LongTable-method                 html  
    idCols                                  html  
    is.items                                html  
    lapply-MultiAssayExperiment-method      html  
    list_or_LongTable-class                 html  
    mcc                                     html  
    merckLongTable                          html  
    metaConstruct                           html  
    metadata-LongTable-method               html  
    metadata-set-LongTable-method           html  
    reindex-LongTable-method                html  
    reindex                                 html  
    rowIDs                                  html  
    rowMeta                                 html  
    sensitivityInfo-set                     html  
    sensitivityInfo                         html  
    sensitivityMeasures-set                 html  
    sensitivityMeasures                     html  
    sensitivityProfiles-set                 html  
    sensitivityProfiles                     html  
    sensitivityRaw-set                      html  
    sensitivityRaw                          html  
    sensitivitySlotToLongTable              html  
    show-CoreSet-method                     html  
    show-LongTable-method                   html  
    showSigAnnot                            html  
    sub-LongTable-ANY-ANY-ANY-method        html  
    sub-subset-LongTable-ANY-ANY-method     html  
    subset-LongTable-method                 html  
    subsetTo                                html  
    summarizeMolecularProfiles              html  
    summarizeSensitivityProfiles            html  
    updateCellId                            html  
** 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
* MD5 sums
packaged installation of 'CoreGx' as CoreGx_1.7.0.zip
* DONE (CoreGx)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'CoreGx' successfully unpacked and MD5 sums checked

Tests output

CoreGx.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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, 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

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   5.65    0.37    6.03 

Example timings

CoreGx.Rcheck/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors1.110.061.18
CoreSet-utils0.250.000.25
CoreSet0.010.000.01
CoreSet20.000.010.02
Create0.080.000.08
LongTable-accessors0.000.020.01
LongTable-class0.190.000.19
LongTable0.010.000.02
LongTableDataMapper-accessors0.020.000.01
LongTableDataMapper-class000
LongTableDataMapper000
amcc 1.34 0.0315.42
as0.280.090.38
as.long.table0.080.000.08
assayCols000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.000.020.01
cash-set-LongTable-method0.000.020.02
checkColumnCardinality0.020.000.01
checkCsetStructure000
colIDs000
colMeta000
connectivityScore0.470.007.05
cosinePerm0.430.006.98
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-intersectList000
dot-symSetDiffList000
dot-unionList000
getIntern000
guessMapping-LongTableDataMapper-method000
gwc0.440.037.72
idCols-LongTable-method000
idCols000
is.items000
mcc0.430.008.42
metaConstruct0.070.000.06
reindex000
rowIDs000
rowMeta000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures0.010.000.02
sensitivityProfiles000
sensitivityRaw000
sensitivitySlotToLongTable000
show-CoreSet-method000
show-LongTable-method0.020.000.01
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.180.010.21
sub-subset-LongTable-ANY-ANY-method0.040.000.03
subset-LongTable-method0.170.000.17
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateCellId0.080.020.09