Benjamin Haibe-Kains
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/PharmacoGx |
| git_branch: devel |
| git_last_commit: ed19577 |
| git_last_commit_date: 2024-02-29 20:56:00 -0400 (Thu, 29 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:06 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 1532/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PharmacoGx 3.7.2 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: PharmacoGx |
| Version: 3.7.2 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings PharmacoGx_3.7.2.tar.gz |
| StartedAt: 2024-03-28 08:15:24 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 08:23:09 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 464.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PharmacoGx.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings PharmacoGx_3.7.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.7.2’
* 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: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
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’
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 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'dot-summarizeSensProfiles.Rd':
.summarizeSensProfiles
Code: function(object, sensitivity.measure = "auc_recomputed",
profiles_assay = "profiles", treatment_col =
"treatmentid", sample_col = "sampleid", cell.lines,
drugs, summary.stat, fill.missing = TRUE)
Docs: function(object, sensitivity.measure = "auc_recomputed",
cell.lines, drugs, summary.stat, fill.missing = TRUE)
Argument names in code not in docs:
profiles_assay treatment_col sample_col
Mismatches in argument names (first 3):
Position: 3 Code: profiles_assay Docs: cell.lines
Position: 4 Code: treatment_col Docs: drugs
Position: 5 Code: sample_col Docs: summary.stat
Codoc mismatches from Rd file 'drugDoseResponseCurve.Rd':
drugDoseResponseCurve
Code: function(drug, cellline, pSets = list(), concentrations =
list(), viabilities = list(), conc_as_log = FALSE,
viability_as_pct = TRUE, trunc = TRUE, legends.label =
c("ic50_published", "gi50_published", "auc_published",
"auc_recomputed", "ic50_recomputed"), ylim = c(0,
100), xlim, mycol, title, plot.type = c("Fitted",
"Actual", "Both"), summarize.replicates = TRUE, lwd =
0.5, cex = 0.7, cex.main = 0.9, legend.loc =
"topright", verbose = TRUE, sample_col = "sampleid",
treatment_col = "treatmentid")
Docs: function(drug, cellline, pSets = list(), concentrations =
list(), viabilities = list(), conc_as_log = FALSE,
viability_as_pct = TRUE, trunc = TRUE, legends.label =
c("ic50_published", "gi50_published", "auc_published",
"auc_recomputed", "ic50_recomputed"), ylim = c(0,
100), xlim, mycol, title, plot.type = c("Fitted",
"Actual", "Both"), summarize.replicates = TRUE, lwd =
0.5, cex = 0.7, cex.main = 0.9, legend.loc =
"topright", verbose = TRUE)
Argument names in code not in docs:
sample_col treatment_col
Codoc mismatches from Rd file 'summarizeSensitivityProfiles-PharmacoSet-method.Rd':
\S4method{summarizeSensitivityProfiles}{PharmacoSet}
Code: function(object, sensitivity.measure = "auc_recomputed",
cell.lines, profiles_assay = "profiles", treatment_col
= "treatmentid", sample_col = "sampleid", drugs,
summary.stat = c("mean", "median", "first", "last",
"max", "min"), fill.missing = TRUE, verbose = TRUE)
Docs: function(object, sensitivity.measure = "auc_recomputed",
cell.lines, drugs, summary.stat = c("mean", "median",
"first", "last", "max", "min"), fill.missing = TRUE,
verbose = TRUE)
Argument names in code not in docs:
profiles_assay treatment_col sample_col
Mismatches in argument names (first 3):
Position: 4 Code: profiles_assay Docs: drugs
Position: 5 Code: treatment_col Docs: summary.stat
Position: 6 Code: sample_col Docs: fill.missing
* 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 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
plot.PharmacoSig 4.273 1.304 2.217
* 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.
PharmacoGx.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘PharmacoGx’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c metaPermC.c -o metaPermC.o
metaPermC.c: In function ‘runPerm’:
metaPermC.c:143:12: warning: unused variable ‘num_larger’ [-Wunused-variable]
143 | uint64_t num_larger = 0;
| ^~~~~~~~~~
metaPermC.c: In function ‘partialCorQUICKSTOP’:
metaPermC.c:328:10: warning: unused variable ‘temp’ [-Wunused-variable]
328 | double temp;
| ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rCPP_bridge.cpp -o rCPP_bridge.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-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)
PharmacoGx.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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, aperm, 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, 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 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")
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[,1] [,2] [,3]
lower_bounds 0 0 0
upper_bounds 1 1 -1
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[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_PharmacoSet_utils.R:28:1'
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
>
> proc.time()
user system elapsed
98.508 2.938 101.727
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
| name | user | system | elapsed | |
| PharmacoSet-accessors | 3.831 | 0.618 | 4.463 | |
| PharmacoSet-utils | 1.745 | 0.024 | 1.773 | |
| PharmacoSet | 0.002 | 0.000 | 0.003 | |
| PharmacoSet2 | 1.247 | 0.020 | 1.270 | |
| PharmacoSig | 0.034 | 0.007 | 0.117 | |
| amcc | 0 | 0 | 0 | |
| availablePSets | 0 | 0 | 0 | |
| callingWaterfall | 0 | 0 | 0 | |
| checkPsetStructure | 1.214 | 0.024 | 1.243 | |
| computeABC | 1.134 | 0.084 | 1.220 | |
| computeAUC | 0.568 | 0.036 | 0.605 | |
| computeAmax | 0.563 | 0.008 | 0.572 | |
| computeBliss | 0 | 0 | 0 | |
| computeHSA | 0 | 0 | 0 | |
| computeICn | 1.129 | 0.040 | 1.170 | |
| computeLoewe | 0 | 0 | 0 | |
| computeSlope | 0.000 | 0.001 | 0.000 | |
| computeZIP | 0.000 | 0.001 | 0.001 | |
| computeZIPdelta-TreatmentResponseExperiment-method | 0 | 0 | 0 | |
| computeZIPdelta | 0.000 | 0.001 | 0.000 | |
| connectivityScore | 3.559 | 0.227 | 3.900 | |
| cosinePerm | 0.111 | 0.072 | 0.103 | |
| dot-computeZIPdelta | 0.001 | 0.000 | 0.000 | |
| downloadPSet | 0 | 0 | 0 | |
| downloadPertSig | 0.000 | 0.000 | 0.001 | |
| drugDoseResponseCurve | 0.000 | 0.000 | 0.001 | |
| drugPerturbationSig | 2.656 | 0.293 | 2.855 | |
| drugSensitivitySig-PharmacoSet-method | 1.438 | 0.111 | 1.551 | |
| effectToDose | 0.000 | 0.000 | 0.001 | |
| filterNoisyCurves | 1.634 | 0.091 | 1.729 | |
| fitTwowayZIP | 0.001 | 0.000 | 0.000 | |
| geneDrugSensitivity | 0 | 0 | 0 | |
| geneDrugSensitivityPBCorr | 0 | 0 | 0 | |
| geneDrugSensitivityPCorr | 0 | 0 | 0 | |
| gwc | 1.167 | 0.051 | 1.284 | |
| hillCurve | 0.001 | 0.000 | 0.001 | |
| intersectPSet | 1.467 | 0.136 | 1.507 | |
| loeweCI | 0.001 | 0.000 | 0.001 | |
| logLogisticRegression | 0.561 | 0.108 | 0.670 | |
| mcc | 0.016 | 0.024 | 3.342 | |
| plot.PharmacoSig | 4.273 | 1.304 | 2.217 | |
| show-PharmacoSet-method | 1.191 | 0.020 | 1.218 | |
| show-PharmacoSig-method | 1.396 | 0.217 | 1.615 | |
| showSigAnnot-PharmacoSig-method | 1.466 | 0.068 | 1.536 | |
| sub-PharmacoSet-ANY-ANY-ANY-method | 1.302 | 0.025 | 1.329 | |
| subsetTo-PharmacoSet-method | 1.309 | 0.012 | 1.324 | |
| summarizeMolecularProfiles-PharmacoSet-method | 0.139 | 0.020 | 0.160 | |
| summarizeSensitivityProfiles-PharmacoSet-method | 0.063 | 0.004 | 0.068 | |