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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for ToxicoGx on tokay2

To the developers/maintainers of the ToxicoGx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ToxicoGx.git to
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raw results

Package 1938/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToxicoGx 1.2.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ToxicoGx
git_branch: RELEASE_3_13
git_last_commit: 04482fe
git_last_commit_date: 2021-06-17 13:42:00 -0400 (Thu, 17 Jun 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: ToxicoGx
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToxicoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ToxicoGx_1.2.1.tar.gz
StartedAt: 2021-10-15 06:46:11 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:51:28 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 317.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ToxicoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToxicoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ToxicoGx_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ToxicoGx.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 'ToxicoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ToxicoGx' version '1.2.1'
* 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 'ToxicoGx' 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
computeLimmaDiffExpr,ToxicoSet: no visible global function definition
  for 'metadata<-'
computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable
  'cell'
Undefined global functions or variables:
  cell metadata<-
* 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 47 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/ToxicoGx.Rcheck/00check.log'
for details.

Installation output

ToxicoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ToxicoGx_1.2.1.tar.gz && rm -rf ToxicoGx.buildbin-libdir && mkdir ToxicoGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ToxicoGx.buildbin-libdir ToxicoGx_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ToxicoGx_1.2.1.zip && rm ToxicoGx_1.2.1.tar.gz ToxicoGx_1.2.1.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
  7 4145k    7  295k    0     0   828k      0  0:00:05 --:--:--  0:00:05  829k
 52 4145k   52 2159k    0     0  1557k      0  0:00:02  0:00:01  0:00:01 1556k
100 4145k  100 4145k    0     0  1901k      0  0:00:02  0:00:02 --:--:-- 1902k

install for i386

* installing *source* package 'ToxicoGx' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ToxicoGx'
    finding HTML links ... done
    HCC_sig                                 html  
    TGGATESsmall                            html  
    ToxicoSet-class                         html  
    ToxicoSet                               html  
    ToxicoSig                               html  
    annotation-set                          html  
    annotation                              html  
    availableTSets                          html  
    checkTSetStructure                      html  
    computeAUC                              html  
    computeICn                              html  
    computeLimmaDiffExpr-ToxicoSet-method   html  
    computeLimmaDiffExpr                    html  
    curation-set                            html  
    curation                                html  
    datasetType-set                         html  
    datasetType                             html  
    dim-ToxicoSet-method                    html  
    downloadTSet                            html  
    drugGeneResponseCurve                   html  
    drugInfo-set                            html  
    drugInfo                                html  
    drugNames-set                           html  
    drugNames                               html  
    drugPerturbationSig                     html  
    drugTimeResponseCurve                   html  
    geneDrugPerturbation                    html  
    logLogisticRegression                   html  
    mDataNames-ToxicoSet-method             html  
    name-ToxicoSet-method                   html  
    sensitivityRaw-set                      html  
    sensitivityRaw                          html  
    sensitivitySlot-set                     html  
    sensitivitySlot                         html  
    show-ToxicoSet-method                   html  
    show-ToxicoSig-method                   html  
    showSigAnnot                            html  
    sub-ToxicoSet-ANY-ANY-ANY-method        html  
    subsetTo                                html  
    summarizeMolecularProfiles              html  
    summarizeSensitivityProfiles            html  
    updateCellId                            html  
    updateDrugId                            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 'ToxicoGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ToxicoGx' as ToxicoGx_1.2.1.zip
* DONE (ToxicoGx)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ToxicoGx' successfully unpacked and MD5 sums checked

Tests output

ToxicoGx.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(ToxicoGx)
Loading required package: 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


Attaching package: 'ToxicoGx'

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

    curation, curation<-, datasetType, datasetType<-, sensitivityRaw,
    sensitivityRaw<-, sensitivitySlot, sensitivitySlot<-, showSigAnnot,
    subsetTo, summarizeMolecularProfiles, summarizeSensitivityProfiles,
    updateCellId

> test_check("ToxicoGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
> 
> proc.time()
   user  system elapsed 
  11.06    0.93   11.96

ToxicoGx.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(ToxicoGx)
Loading required package: 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


Attaching package: 'ToxicoGx'

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

    curation, curation<-, datasetType, datasetType<-, sensitivityRaw,
    sensitivityRaw<-, sensitivitySlot, sensitivitySlot<-, showSigAnnot,
    subsetTo, summarizeMolecularProfiles, summarizeSensitivityProfiles,
    updateCellId

> test_check("ToxicoGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
> 
> proc.time()
   user  system elapsed 
  11.71    0.59   13.50

Example timings

ToxicoGx.Rcheck/examples_i386/ToxicoGx-Ex.timings

nameusersystemelapsed
ToxicoSet-class2.370.272.64
annotation-set0.060.000.07
annotation0.050.010.07
availableTSets000
checkTSetStructure0.060.050.11
computeAUC0.520.030.55
computeICn0.910.000.90
computeLimmaDiffExpr-ToxicoSet-method000
curation-set0.060.000.07
curation0.080.000.07
datasetType-set0.060.000.07
dim-ToxicoSet-method0.050.020.06
downloadTSet000
drugGeneResponseCurve000
drugInfo-set0.530.010.55
drugInfo0.060.000.06
drugNames-set0.080.020.09
drugNames0.040.030.08
drugPerturbationSig000
drugTimeResponseCurve0.150.020.16
geneDrugPerturbation1.790.061.86
logLogisticRegression0.490.000.48
mDataNames-ToxicoSet-method000
name-ToxicoSet-method000
sensitivityRaw-set0.000.010.02
sensitivityRaw0.090.020.11
show-ToxicoSet-method0.020.000.01
show-ToxicoSig-method0.290.000.30
showSigAnnot0.270.050.31
sub-ToxicoSet-ANY-ANY-ANY-method0.030.000.03
subsetTo0.050.000.05
summarizeMolecularProfiles0.650.010.67
summarizeSensitivityProfiles0.080.000.08
updateCellId0.090.020.12
updateDrugId0.110.000.11

ToxicoGx.Rcheck/examples_x64/ToxicoGx-Ex.timings

nameusersystemelapsed
ToxicoSet-class2.360.252.61
annotation-set0.070.000.08
annotation0.070.020.07
availableTSets000
checkTSetStructure0.110.000.11
computeAUC0.500.030.53
computeICn0.930.030.97
computeLimmaDiffExpr-ToxicoSet-method000
curation-set0.050.020.07
curation0.060.010.07
datasetType-set0.070.000.07
dim-ToxicoSet-method0.060.000.06
downloadTSet0.010.000.01
drugGeneResponseCurve000
drugInfo-set0.050.020.07
drugInfo0.060.000.06
drugNames-set0.100.000.09
drugNames0.090.010.11
drugPerturbationSig000
drugTimeResponseCurve0.140.020.16
geneDrugPerturbation1.830.001.83
logLogisticRegression0.660.010.67
mDataNames-ToxicoSet-method000
name-ToxicoSet-method000
sensitivityRaw-set0.000.020.01
sensitivityRaw0.120.030.16
show-ToxicoSet-method000
show-ToxicoSig-method0.480.020.50
showSigAnnot0.330.000.32
sub-ToxicoSet-ANY-ANY-ANY-method0.050.000.05
subsetTo0.040.000.05
summarizeMolecularProfiles0.830.010.84
summarizeSensitivityProfiles0.110.020.13
updateCellId0.190.030.22
updateDrugId0.110.010.12