| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).
| 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" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1567/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PharmacoGx 3.12.2 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: PharmacoGx |
| Version: 3.12.2 |
| 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_3.12.2.tar.gz |
| StartedAt: 2025-08-15 05:21:41 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 05:30:32 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 530.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PharmacoGx.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.12.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* 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 '3.12.2'
* 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 whether package 'PharmacoGx' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 8.12 2.09 10.22
connectivityScore 2.74 0.06 17.15
gwc 2.22 0.03 17.18
mcc 0.92 0.00 18.11
cosinePerm 0.86 0.02 15.36
* 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.
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' ... ** this is package 'PharmacoGx' version '3.12.2' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' 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:/rtools45/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:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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:/rtools45/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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/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)
PharmacoGx.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 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 UHNBreast 2020-06-24T14:39:26.588Z UHNBreast_2019 2019
2 PDTX 2022-01-07T00:00:00.000Z PDTX_2019 2019
3 PRISM 2021-08-18T16:28:45.207Z PRISM_2020 2020
4 gCSI 2021-06-11T21:58:16.390Z gCSI_2019 2019
5 GRAY 2021-02-23T14:39:26.588Z GRAY_2017 2017
6 GDSC 2021-12-16T19:58:28.388Z GDSC_2020(v2-8.2) 2020(v2-8.2)
7 FIMM 2020-06-24T14:39:26.588Z FIMM_2016 2016
8 NCI60 2021-08-18T16:28:45.207Z NCI60_2021 2021
9 GDSC 2021-12-16T19:10:35.091Z GDSC_2020(v1-8.2) 2020(v1-8.2)
10 CTRPv2 2020-06-24T14:39:26.588Z CTRPv2_2015 2015
11 Tavor 2021-03-05T17:05:08.535Z Tavor_2020 2020
12 BeatAML 2021-03-05T16:55:27.968Z BeatAML_2018 2018
13 CCLE 2020-06-24T14:39:26.588Z CCLE_2015 2015
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 both Mammolit.... 10.5281/zenodo.7826860
2 <NA> Bruna, A.... 10.5281/zenodo.7826875
3 sensitivity Corsello.... 10.5281/zenodo.7826864
4 <NA> Petr Smi.... 10.5281/zenodo.7829857
5 sensitivity Hafner, .... 10.5281/zenodo.7826847
6 sensitivity c("Yang,.... 10.5281/zenodo.5787145
7 sensitivity Mpindi, .... 10.5281/zenodo.7823755
8 sensitivity Shoemake.... 10.5281/zenodo.7893032
9 sensitivity c("Yang,.... 10.5281/zenodo.7829915
10 sensitivity c("Rees,.... 10.5281/zenodo.7826870
11 sensitivity Sigal Ta.... 10.5281/zenodo.5979590
12 sensitivity Tyner, J.... 10.5281/zenodo.7829853
13 sensitivity Barretin.... 10.5281/zenodo.3905461
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/record/7826860/files/PSet_UHNBreast.rds?download=1
2 https://zenodo.org/record/7826875/files/PSet_PDTXBreast.rds?download=1
3 https://zenodo.org/record/7826864/files/PSet_PRISM.rds?download=1
4 https://zenodo.org/record/7829857/files/PSet_gCSI2019.rds?download=1
5 https://zenodo.org/record/7826847/files/PSet_GRAY2017.rds?download=1
6 https://zenodo.org/records/5787145/files/GDSC2.rds?download=1
7 https://zenodo.org/record/7823755/files/PSet_FIMM.rds?download=1
8 https://zenodo.org/record/7893032/files/PSet_NCI60.rds?download=1
9 https://zenodo.org/record/7829915/files/PSet_GDSC2020.rds?download=1
10 https://zenodo.org/record/7826870/files/PSet_CTRPv2.rds?download=1
11 https://zenodo.org/record/5979590/files/Tavor.rds?download=1
12 https://zenodo.org/record/7829853/files/PSet_BeatAML.rds?download=1
13 https://zenodo.org/record/3905462/files/CCLE.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
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
[1] 1 1 -1
[1] 0
[1] 0
[,1] [,2] [,3]
lower_bounds 0 0 0
upper_bounds 1 1 -1
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
[ 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
85.14 2.26 88.07
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
| name | user | system | elapsed | |
| PharmacoSet-accessors | 8.12 | 2.09 | 10.22 | |
| PharmacoSet-utils | 1.89 | 0.07 | 1.95 | |
| PharmacoSet | 0.00 | 0.02 | 0.01 | |
| PharmacoSet2 | 1.22 | 0.06 | 1.28 | |
| PharmacoSig | 0.01 | 0.05 | 0.06 | |
| amcc | 0 | 0 | 0 | |
| availablePSets | 0 | 0 | 0 | |
| callingWaterfall | 0 | 0 | 0 | |
| checkPsetStructure | 0.93 | 0.08 | 1.00 | |
| computeABC | 0.92 | 0.03 | 0.96 | |
| computeAUC | 0.4 | 0.0 | 0.4 | |
| computeAmax | 0.5 | 0.0 | 0.5 | |
| computeBliss | 0 | 0 | 0 | |
| computeHSA | 0 | 0 | 0 | |
| computeICn | 0.97 | 0.01 | 0.99 | |
| computeLoewe | 0 | 0 | 0 | |
| computeSlope | 0 | 0 | 0 | |
| computeZIP | 0 | 0 | 0 | |
| computeZIPdelta-TreatmentResponseExperiment-method | 0 | 0 | 0 | |
| computeZIPdelta | 0 | 0 | 0 | |
| connectivityScore | 2.74 | 0.06 | 17.15 | |
| cosinePerm | 0.86 | 0.02 | 15.36 | |
| dot-computeZIPdelta | 0 | 0 | 0 | |
| downloadPSet | 0 | 0 | 0 | |
| downloadPertSig | 0 | 0 | 0 | |
| drugDoseResponseCurve | 0 | 0 | 0 | |
| drugPerturbationSig | 1.89 | 0.15 | 2.05 | |
| drugSensitivitySig-PharmacoSet-method | 1.51 | 0.05 | 1.56 | |
| effectToDose | 0 | 0 | 0 | |
| filterNoisyCurves | 1.41 | 0.01 | 1.42 | |
| fitTwowayZIP | 0 | 0 | 0 | |
| geneDrugSensitivity | 0 | 0 | 0 | |
| geneDrugSensitivityPBCorr | 0 | 0 | 0 | |
| geneDrugSensitivityPCorr | 0 | 0 | 0 | |
| gwc | 2.22 | 0.03 | 17.18 | |
| hillCurve | 0 | 0 | 0 | |
| intersectPSet | 1.53 | 0.03 | 1.56 | |
| loeweCI | 0 | 0 | 0 | |
| logLogisticRegression | 0.44 | 0.00 | 0.44 | |
| mcc | 0.92 | 0.00 | 18.11 | |
| plot.PharmacoSig | 1.96 | 0.05 | 2.03 | |
| show-PharmacoSet-method | 1.22 | 0.05 | 1.27 | |
| show-PharmacoSig-method | 1.48 | 0.01 | 1.50 | |
| showSigAnnot-PharmacoSig-method | 1.33 | 0.03 | 1.36 | |
| sub-PharmacoSet-ANY-ANY-ANY-method | 1.36 | 0.03 | 1.39 | |
| subsetTo-PharmacoSet-method | 1.19 | 0.04 | 1.21 | |
| summarizeMolecularProfiles-PharmacoSet-method | 0.18 | 0.00 | 0.19 | |
| summarizeSensitivityProfiles-PharmacoSet-method | 0.05 | 0.03 | 0.08 | |
| updateObject-PharmacoSet-method | 0.11 | 0.00 | 0.11 | |