Multiple platform build/check report for BioC 3.21 - CHECK results for PharmacoGx on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 PharmacoGx on kjohnson1

To the developers/maintainers of the PharmacoGx package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: PharmacoGx

Version: 3.12.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PharmacoGx_3.12.2.tar.gz

StartedAt: 2025-10-15 07:24:55 -0400 (Wed, 15 Oct 2025)

EndedAt: 2025-10-15 07:31:36 -0400 (Wed, 15 Oct 2025)

EllapsedTime: 400.8 seconds

RetCode: 0

Status: OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PharmacoGx_3.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.12.2’
* 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 ‘PharmacoGx’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.Hill’ ‘.summarizeSensitivityNumbers’ ‘partialCorQUICKSTOP’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeZIPdelta: no visible binding for global variable
  ‘EC50_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable
  ‘EC50_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘HS_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable
  ‘HS_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘E_inf_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘E_inf_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable ‘Rsqr_1_to_2’
.computeZIPdelta: no visible binding for global variable ‘Rsqr_2_to_1’
.plotProjHill: no visible binding for global variable ‘treatment1id’
.plotProjHill: no visible binding for global variable ‘treatment2id’
.plotProjHill: no visible binding for global variable ‘treatment2dose’
.plotProjHill: no visible binding for global variable
  ‘EC50_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘HS_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘EC50_2’
.plotProjHill: no visible binding for global variable ‘E_inf_2’
.plotProjHill: no visible binding for global variable
  ‘E_inf_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘HS_2’
.plotProjHill: no visible binding for global variable ‘treatment1dose’
.plotProjHill: no visible binding for global variable ‘combo_viability’
.plotProjHill: no visible binding for global variable ‘x’
.plotProjHill: no visible binding for global variable
  ‘EC50_proj_1_to_2’
.plotProjHill: no visible binding for global variable ‘HS_proj_1_to_2’
.plotProjHill: no visible binding for global variable ‘EC50_1’
.plotProjHill: no visible binding for global variable ‘HS_1’
.plotProjHill: no visible binding for global variable ‘E_inf_1’
.plotProjHill: no visible binding for global variable
  ‘E_inf_proj_1_to_2’
PharmacoSet2: no visible global function definition for
  ‘MultiAssayExperiment’
fitTwowayZIP: no visible binding for global variable ‘treatment1dose’
fitTwowayZIP: no visible binding for global variable ‘combo_viability’
fitTwowayZIP: no visible binding for global variable ‘treatment2dose’
fitTwowayZIP: no visible binding for global variable ‘EC50_2’
fitTwowayZIP: no visible binding for global variable ‘HS_2’
fitTwowayZIP: no visible binding for global variable ‘E_inf_2’
fitTwowayZIP: no visible binding for global variable ‘EC50_1’
fitTwowayZIP: no visible binding for global variable ‘HS_1’
fitTwowayZIP: no visible binding for global variable ‘E_inf_1’
mergePSets: no visible global function definition for
  ‘checkPSetStructure’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘ZIP’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘treatment1dose’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘treatment2dose’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘Rsqr_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘Rsqr_2_to_1’
Undefined global functions or variables:
  EC50_1 EC50_2 EC50_proj_1_to_2 EC50_proj_2_to_1 E_inf_1 E_inf_2
  E_inf_proj_1_to_2 E_inf_proj_2_to_1 HS_1 HS_2 HS_proj_1_to_2
  HS_proj_2_to_1 MultiAssayExperiment Rsqr_1_to_2 Rsqr_2_to_1 ZIP
  checkPSetStructure combo_viability treatment1dose treatment1id
  treatment2dose treatment2id x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  computeZIPdelta-TreatmentResponseExperiment-method.Rd:
    TreatmentResponseExperiment
  fitTwowayZIP.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
PharmacoSet-accessors 4.122  2.882   7.033
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.

Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘PharmacoGx’ ...
** this is package ‘PharmacoGx’ version ‘3.12.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c metaPermC.c -o metaPermC.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rCPP_bridge.cpp -o rCPP_bridge.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-PharmacoGx/00new/PharmacoGx/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PharmacoGx)

Tests output

PharmacoGx.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from 'package:utils':

    findMatches

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


Attaching package: 'PharmacoGx'

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

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

> 
> test_check("PharmacoGx")
   Dataset Name             Date Created         PSet Name      version
1          GDSC 2021-12-16T19:58:28.388Z GDSC_2020(v2-8.2) 2020(v2-8.2)
2          FIMM 2020-06-24T14:39:26.588Z         FIMM_2016         2016
3         Tavor 2021-03-05T17:05:08.535Z        Tavor_2020         2020
4         NCI60 2021-08-18T16:28:45.207Z        NCI60_2021         2021
5     UHNBreast 2020-06-24T14:39:26.588Z    UHNBreast_2019         2019
6          GDSC 2021-12-16T19:10:35.091Z GDSC_2020(v1-8.2) 2020(v1-8.2)
7         PRISM 2021-08-18T16:28:45.207Z        PRISM_2020         2020
8       BeatAML 2021-03-05T16:55:27.968Z      BeatAML_2018         2018
9          gCSI 2021-06-11T21:58:16.390Z         gCSI_2019         2019
10       CTRPv2 2020-06-24T14:39:26.588Z       CTRPv2_2015         2015
11         GRAY 2021-02-23T14:39:26.588Z         GRAY_2017         2017
12         CCLE 2020-06-24T14:39:26.588Z         CCLE_2015         2015
13         PDTX 2022-01-07T00:00:00.000Z         PDTX_2019         2019
14          GBM 2022-01-07T00:00:00.000Z          GBM_scr2         2021
15          GBM 2022-01-07T00:00:00.000Z          GBM_scr3         2021
16   NCISarcoma                     <NA>   NCISarcoma_2015         2015
17        TCL38 2024-11-20T14:46:07.030Z             TCL38         2015
          type  publication                     DOI
1  sensitivity c("Yang,....  10.5281/zenodo.5787145
2  sensitivity Mpindi, ....  10.5281/zenodo.7823755
3  sensitivity Sigal Ta....  10.5281/zenodo.5979590
4  sensitivity Shoemake....  10.5281/zenodo.7893032
5         both Mammolit....  10.5281/zenodo.7826860
6  sensitivity c("Yang,....  10.5281/zenodo.7829915
7  sensitivity Corsello....  10.5281/zenodo.7826864
8  sensitivity Tyner, J....  10.5281/zenodo.7829853
9         <NA> Petr Smi....  10.5281/zenodo.7829857
10 sensitivity c("Rees,....  10.5281/zenodo.7826870
11 sensitivity Hafner, ....  10.5281/zenodo.7826847
12 sensitivity Barretin....  10.5281/zenodo.3905461
13        <NA> Bruna, A....  10.5281/zenodo.7826875
14        <NA>               10.5281/zenodo.7829873
15        <NA>               10.5281/zenodo.7829873
16        <NA> Bruna, A....                        
17        <NA>           ,  10.5281/zenodo.14733210
                                                                 Download
1           https://zenodo.org/records/5787145/files/GDSC2.rds?download=1
2        https://zenodo.org/record/7823755/files/PSet_FIMM.rds?download=1
3            https://zenodo.org/record/5979590/files/Tavor.rds?download=1
4       https://zenodo.org/record/7893032/files/PSet_NCI60.rds?download=1
5   https://zenodo.org/record/7826860/files/PSet_UHNBreast.rds?download=1
6    https://zenodo.org/record/7829915/files/PSet_GDSC2020.rds?download=1
7       https://zenodo.org/record/7826864/files/PSet_PRISM.rds?download=1
8     https://zenodo.org/record/7829853/files/PSet_BeatAML.rds?download=1
9    https://zenodo.org/record/7829857/files/PSet_gCSI2019.rds?download=1
10     https://zenodo.org/record/7826870/files/PSet_CTRPv2.rds?download=1
11   https://zenodo.org/record/7826847/files/PSet_GRAY2017.rds?download=1
12            https://zenodo.org/record/3905462/files/CCLE.rds?download=1
13 https://zenodo.org/record/7826875/files/PSet_PDTXBreast.rds?download=1
14   https://zenodo.org/record/7829873/files/PSet_GBM_scr2.rds?download=1
15   https://zenodo.org/record/7829873/files/PSet_GBM_scr3.rds?download=1
16                                                                       
17    https://zenodo.org/records/14733210/files/TCL38_PSet.RDS?download=1

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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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[ FAIL 0 | WARN 3 | SKIP 1 | PASS 132 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_PharmacoSet_utils.R:28:1'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 67.821   1.350  70.712

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

name	user	system	elapsed
PharmacoSet-accessors	4.122	2.882	7.033
PharmacoSet-utils	1.749	0.025	1.774
PharmacoSet	0.003	0.000	0.004
PharmacoSet2	1.289	0.021	1.312
PharmacoSig	0.030	0.011	0.041
amcc	0	0	0
availablePSets	0	0	0
callingWaterfall	0	0	0
checkPsetStructure	1.751	0.025	1.781
computeABC	0.516	0.020	0.537
computeAUC	0.325	0.008	0.333
computeAmax	0.326	0.002	0.328
computeBliss	0.000	0.000	0.001
computeHSA	0.000	0.000	0.001
computeICn	0.647	0.003	0.651
computeLoewe	0	0	0
computeSlope	0.000	0.000	0.001
computeZIP	0.000	0.000	0.001
computeZIPdelta-TreatmentResponseExperiment-method	0.000	0.001	0.000
computeZIPdelta	0.000	0.000	0.001
connectivityScore	3.928	0.114	4.034
cosinePerm	0.048	0.091	0.134
dot-computeZIPdelta	0	0	0
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0.001	0.000	0.001
drugPerturbationSig	1.790	0.211	2.037
drugSensitivitySig-PharmacoSet-method	0.973	0.042	1.020
effectToDose	0	0	0
filterNoisyCurves	0.893	0.025	0.922
fitTwowayZIP	0	0	0
geneDrugSensitivity	0.000	0.001	0.000
geneDrugSensitivityPBCorr	0	0	0
geneDrugSensitivityPCorr	0	0	0
gwc	1.273	0.154	1.451
hillCurve	0.001	0.001	0.001
intersectPSet	1.458	0.139	1.605
loeweCI	0.000	0.000	0.001
logLogisticRegression	0.366	0.098	0.465
mcc	0.011	0.027	1.863
plot.PharmacoSig	2.673	0.697	1.531
show-PharmacoSet-method	0.624	0.053	0.686
show-PharmacoSig-method	1.075	0.046	1.128
showSigAnnot-PharmacoSig-method	0.968	0.036	1.008
sub-PharmacoSet-ANY-ANY-ANY-method	1.158	0.022	1.183
subsetTo-PharmacoSet-method	0.527	0.040	0.576
summarizeMolecularProfiles-PharmacoSet-method	0.065	0.006	0.071
summarizeSensitivityProfiles-PharmacoSet-method	0.036	0.004	0.041
updateObject-PharmacoSet-method	0.130	0.009	0.139