Multiple platform build/check report for BioC 3.21 - CHECK results for PharmacoGx on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4760
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4479
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4443
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4391
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 palomino7

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: 3.11.1

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PharmacoGx.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PharmacoGx_3.11.1.tar.gz

StartedAt: 2025-01-11 04:04:56 -0500 (Sat, 11 Jan 2025)

EndedAt: 2025-01-11 04:13:08 -0500 (Sat, 11 Jan 2025)

EllapsedTime: 492.0 seconds

RetCode: 0

Status: OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PharmacoGx.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PharmacoGx_3.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '3.11.1'
* 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 'PharmacoGx' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/PharmacoGx/libs/x64/PharmacoGx.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
PharmacoSet-accessors 6.91   1.94    8.84
connectivityScore     2.52   0.05   16.77
gwc                   1.95   0.01   14.82
cosinePerm            0.83   0.03   14.67
mcc                   0.78   0.04   14.91
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.

Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'PharmacoGx' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c metaPermC.c -o metaPermC.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c rCPP_bridge.cpp -o rCPP_bridge.o
g++ -std=gnu++17 -shared -s -static-libgcc -o PharmacoGx.dll tmp.def RcppExports.o metaPermC.o rCPP_bridge.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-PharmacoGx/00new/PharmacoGx/libs/x64
** 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
** 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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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")
   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.14528245
                                                                 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/14528245/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 
  82.17    1.89   84.71

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

name	user	system	elapsed
PharmacoSet-accessors	6.91	1.94	8.84
PharmacoSet-utils	1.60	0.03	1.62
PharmacoSet	0	0	0
PharmacoSet2	1.38	0.05	1.42
PharmacoSig	0.03	0.03	0.06
amcc	0	0	0
availablePSets	0	0	0
callingWaterfall	0	0	0
checkPsetStructure	0.93	0.02	0.95
computeABC	0.72	0.04	0.77
computeAUC	0.39	0.00	0.39
computeAmax	0.33	0.00	0.33
computeBliss	0	0	0
computeHSA	0	0	0
computeICn	1.02	0.00	1.01
computeLoewe	0	0	0
computeSlope	0	0	0
computeZIP	0.01	0.00	0.02
computeZIPdelta-TreatmentResponseExperiment-method	0	0	0
computeZIPdelta	0	0	0
connectivityScore	2.52	0.05	16.77
cosinePerm	0.83	0.03	14.67
dot-computeZIPdelta	0	0	0
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0	0	0
drugPerturbationSig	2.15	0.04	2.21
drugSensitivitySig-PharmacoSet-method	1.21	0.04	1.23
effectToDose	0	0	0
filterNoisyCurves	1.20	0.03	1.23
fitTwowayZIP	0	0	0
geneDrugSensitivity	0	0	0
geneDrugSensitivityPBCorr	0	0	0
geneDrugSensitivityPCorr	0	0	0
gwc	1.95	0.01	14.82
hillCurve	0.00	0.02	0.01
intersectPSet	1.58	0.04	1.63
loeweCI	0	0	0
logLogisticRegression	0.28	0.00	0.28
mcc	0.78	0.04	14.91
plot.PharmacoSig	1.88	0.03	1.90
show-PharmacoSet-method	1.11	0.01	1.13
show-PharmacoSig-method	1.20	0.05	1.25
showSigAnnot-PharmacoSig-method	1.31	0.05	1.36
sub-PharmacoSet-ANY-ANY-ANY-method	1.36	0.03	1.39
subsetTo-PharmacoSet-method	1.08	0.06	1.14
summarizeMolecularProfiles-PharmacoSet-method	0.11	0.03	0.14
summarizeSensitivityProfiles-PharmacoSet-method	0.08	0.02	0.09
updateObject-PharmacoSet-method	0.14	0.00	0.14