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This page was generated on 2021-11-26 14:05:14 -0500 (Fri, 26 Nov 2021).

CHECK results for PharmacoGx on riesling1

To the developers/maintainers of the PharmacoGx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PharmacoGx.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 1393/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PharmacoGx 2.7.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-25 14:50:11 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/PharmacoGx
git_branch: master
git_last_commit: f3d1fbf
git_last_commit_date: 2021-10-26 12:29:36 -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 'CoreGx' which is not available

Summary

Package: PharmacoGx
Version: 2.7.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PharmacoGx_2.7.0.tar.gz
StartedAt: 2021-11-26 02:59:35 -0500 (Fri, 26 Nov 2021)
EndedAt: 2021-11-26 03:04:55 -0500 (Fri, 26 Nov 2021)
EllapsedTime: 319.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PharmacoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PharmacoGx_2.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PharmacoGx.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 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '2.7.0'
* 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 'PharmacoGx' 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 ... OK
* 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 2251 marked UTF-8 strings
* 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              1.50   0.03   16.35
gwc               1.18   0.02    8.25
mcc               0.52   0.02    8.67
connectivityScore 0.50   0.00    7.12
cosinePerm        0.46   0.00    7.72
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.



Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/PharmacoGx_2.7.0.tar.gz && rm -rf PharmacoGx.buildbin-libdir && mkdir PharmacoGx.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PharmacoGx.buildbin-libdir PharmacoGx_2.7.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PharmacoGx_2.7.0.zip && rm PharmacoGx_2.7.0.tar.gz PharmacoGx_2.7.0.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
 40 3573k   40 1443k    0     0  2454k      0  0:00:01 --:--:--  0:00:01 2450k
100 3573k  100 3573k    0     0  3148k      0  0:00:01  0:00:01 --:--:-- 3148k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'PharmacoGx' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PharmacoGx'
    finding HTML links ... done
    CCLEsmall                               html  
    CMAPsmall                               html  
    GDSCsmall                               html  
    HDAC_genes                              html  
    PharmacoSet-accessors                   html  
    PharmacoSet-class                       html  
    PharmacoSet-utils                       html  
    PharmacoSet                             html  
    PharmacoSet2                            html  
    PharmacoSig                             html  
    amcc                                    html  
    availablePSets                          html  
    callingWaterfall                        html  
    checkPsetStructure                      html  
    computeABC                              html  
    computeAUC                              html  
    computeAmax                             html  
    computeICn                              html  
    computeSlope                            html  
    connectivityScore                       html  
    cosinePerm                              html  
    dim-PharmacoSet-method                  html  
    dot-summarizeSensProfiles               html  
    downloadPSet                            html  
    downloadPertSig                         html  
    drugDoseResponseCurve                   html  
    drugInfo-set                            html  
    drugInfo                                html  
    drugNames-set                           html  
    drugNames                               html  
    drugPerturbationSig                     html  
    drugSensitivitySig-PharmacoSet-method   html  
    filterNoisyCurves                       html  
    geneDrugSensitivity                     html  
    gwc                                     html  
    intersectPSet                           html  
    logLogisticRegression                   html  
    mcc                                     html  
    plot.PharmacoSig                        html  
    show-PharmacoSet-method                 html  
    show-PharmacoSig-method                 html  
    showSigAnnot-PharmacoSig-method         html  
    sub-PharmacoSet-ANY-ANY-ANY-method      html  
    subsetTo-PharmacoSet-method             html  
    summarizeMolecularProfiles-PharmacoSet-method
                                            html  
    summarizeSensitivityProfiles-PharmacoSet-method
                                            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 'PharmacoGx' as PharmacoGx_2.7.0.zip
* DONE (PharmacoGx)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'PharmacoGx' successfully unpacked and MD5 sums checked

Tests output

PharmacoGx.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.

> Sys.unsetenv("R_TESTS")
> 
> library(testthat)
> library(PharmacoGx)
Loading required package: 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


Attaching package: 'PharmacoGx'

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

    .parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc

> 
> test_check("PharmacoGx")
[1] NA  3
[1]   1   2 Inf
[1] NA  3
[1]   1   2 Inf

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[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

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== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
  45.60    0.73   46.32 

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
PharmacoSet-accessors2.421.153.58
PharmacoSet-utils1.410.071.47
PharmacoSet000
PharmacoSet20.650.030.68
amcc 1.50 0.0316.35
availablePSets000
callingWaterfall000
checkPsetStructure0.670.030.70
computeABC0.460.130.58
computeAUC0.290.000.30
computeAmax0.320.000.31
computeICn0.610.000.61
computeSlope000
connectivityScore0.500.007.12
cosinePerm0.460.007.72
downloadPSet000
downloadPertSig000
drugDoseResponseCurve000
drugNames-set0.650.030.67
drugNames0.650.000.66
drugPerturbationSig1.270.041.31
drugSensitivitySig-PharmacoSet-method0.730.000.74
filterNoisyCurves0.490.000.48
gwc1.180.028.25
intersectPSet0.770.030.80
logLogisticRegression0.310.000.31
mcc0.520.028.67
plot.PharmacoSig0.830.040.88
show-PharmacoSet-method0.650.020.67
show-PharmacoSig-method0.640.010.66
showSigAnnot-PharmacoSig-method0.660.040.68
sub-PharmacoSet-ANY-ANY-ANY-method0.650.040.71
subsetTo-PharmacoSet-method0.710.030.73
summarizeMolecularProfiles-PharmacoSet-method0.090.000.09
summarizeSensitivityProfiles-PharmacoSet-method0.030.020.05