Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-13 15:05:20 -0400 (Wed, 13 Oct 2021).

CHECK results for CoreGx on tokay2

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 1.4.2  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_13
git_last_commit: 32dc73a
git_last_commit_date: 2021-09-28 16:58:37 -0400 (Tue, 28 Sep 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: 1.4.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoreGx_1.4.2.tar.gz
StartedAt: 2021-10-12 21:14:40 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 21:19:31 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 291.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoreGx_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoreGx.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-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/3.13/bioc/src/contrib/CoreGx_1.4.2.tar.gz && rm -rf CoreGx.buildbin-libdir && mkdir CoreGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoreGx.buildbin-libdir CoreGx_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CoreGx_1.4.2.zip && rm CoreGx_1.4.2.tar.gz CoreGx_1.4.2.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
100 1200k  100 1200k    0     0  2382k      0 --:--:-- --:--:-- --:--:-- 2386k

install for i386

* 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                                 html  
    Create                                  html  
    DataMapper-accessors                    html  
    DataMapper-class                        html  
    LongTable-class                         html  
    LongTable                               html  
    LongTableDataMapper-accessors           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CoreGx.buildbin-libdir/00LOCK-CoreGx/00new/CoreGx/help/assayMap+2CLongTableDataMapper+2CList-method.html
    LongTableDataMapper-class               html  
    LongTableDataMapper                     html  
    amcc                                    html  
    as                                      html  
    as.data.frame.LongTable                 html  
    as.data.table.LongTable                 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-convertCSetMolecularProfilesToSE    html  
    dot-distancePointLine                   html  
    dot-distancePointSegment                html  
    dot-intersectList                       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

install for x64

* installing *source* package 'CoreGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoreGx' as CoreGx_1.4.2.zip
* DONE (CoreGx)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CoreGx' successfully unpacked and MD5 sums checked

Tests output

CoreGx.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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 
   7.85    0.92    8.75 

CoreGx.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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

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 
   8.75    0.51    9.25 

Example timings

CoreGx.Rcheck/examples_i386/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors1.320.081.39
Create0.040.050.07
LongTable-class1.030.051.08
LongTableDataMapper-accessors0.010.000.01
LongTableDataMapper-class000
amcc1.270.011.29
as0.170.030.20
as.data.frame.LongTable0.290.130.43
as.long.table0.080.010.11
assayCols000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.030.000.03
cash-set-LongTable-method0.090.050.14
checkColumnCardinality000
checkCsetStructure0.080.000.08
colIDs000
colMeta000
connectivityScore0.060.000.06
cosinePerm0.050.000.05
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-intersectList000
dot-symSetDiffList000
dot-unionList000
getIntern000
guessMapping-LongTableDataMapper-method0.020.000.01
gwc0.110.000.11
idCols-LongTable-method000
idCols000
is.items000
mcc1.480.011.50
metaConstruct0.080.020.09
reindex000
rowIDs000
rowMeta000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures000
sensitivityProfiles000
sensitivityRaw000
sensitivitySlotToLongTable000
show-CoreSet-method0.030.000.04
show-LongTable-method000
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.340.000.34
sub-subset-LongTable-ANY-ANY-method0.110.010.12
subset-LongTable-method0.320.020.33
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateCellId0.280.040.33

CoreGx.Rcheck/examples_x64/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-accessors2.120.082.20
Create0.080.000.08
LongTable-class0.420.020.46
LongTableDataMapper-accessors000
LongTableDataMapper-class0.020.000.01
amcc1.300.011.31
as0.110.020.13
as.data.frame.LongTable0.210.080.30
as.long.table0.080.000.08
assayCols000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.020.000.01
cash-set-LongTable-method0.120.010.11
checkColumnCardinality000
checkCsetStructure0.100.000.09
colIDs000
colMeta000
connectivityScore0.070.000.08
cosinePerm0.040.000.03
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-intersectList000
dot-symSetDiffList000
dot-unionList000
getIntern000
guessMapping-LongTableDataMapper-method0.020.000.01
gwc0.140.000.15
idCols-LongTable-method000
idCols000
is.items000
mcc1.670.041.70
metaConstruct0.080.000.08
reindex000
rowIDs000
rowMeta000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures000
sensitivityProfiles000
sensitivityRaw000
sensitivitySlotToLongTable000
show-CoreSet-method0.030.000.03
show-LongTable-method0.030.000.03
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.520.000.52
sub-subset-LongTable-ANY-ANY-method0.110.020.11
subset-LongTable-method0.290.010.31
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateCellId0.270.020.28