Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
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" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1529/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PharmacoGx 3.11.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 3.11.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PharmacoGx_3.11.0.tar.gz |
StartedAt: 2024-12-24 00:53:44 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 01:00:29 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 404.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PharmacoGx.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PharmacoGx_3.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PharmacoGx’ version ‘3.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘PharmacoGx’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 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 loading without being on the library search path ... 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 ... INFO 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 PharmacoSet-accessors 2.964 3.557 6.521 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck/00check.log’ for details.
PharmacoGx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PharmacoGx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘PharmacoGx’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c metaPermC.c -o metaPermC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c rCPP_bridge.cpp -o rCPP_bridge.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/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) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 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") | | | 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 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 64.222 2.181 66.472
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
name | user | system | elapsed | |
PharmacoSet-accessors | 2.964 | 3.557 | 6.521 | |
PharmacoSet-utils | 1.418 | 0.045 | 1.463 | |
PharmacoSet | 0.002 | 0.000 | 0.003 | |
PharmacoSet2 | 1.878 | 0.122 | 2.001 | |
PharmacoSig | 0.030 | 0.017 | 0.118 | |
amcc | 0 | 0 | 0 | |
availablePSets | 0 | 0 | 0 | |
callingWaterfall | 0 | 0 | 0 | |
checkPsetStructure | 1.082 | 0.044 | 1.128 | |
computeABC | 0.635 | 0.084 | 0.719 | |
computeAUC | 0.302 | 0.000 | 0.303 | |
computeAmax | 0.304 | 0.000 | 0.306 | |
computeBliss | 0 | 0 | 0 | |
computeHSA | 0.000 | 0.000 | 0.001 | |
computeICn | 0.618 | 0.001 | 0.618 | |
computeLoewe | 0.000 | 0.000 | 0.001 | |
computeSlope | 0.001 | 0.001 | 0.001 | |
computeZIP | 0.000 | 0.000 | 0.001 | |
computeZIPdelta-TreatmentResponseExperiment-method | 0 | 0 | 0 | |
computeZIPdelta | 0 | 0 | 0 | |
connectivityScore | 3.532 | 0.274 | 3.885 | |
cosinePerm | 0.061 | 0.116 | 0.116 | |
dot-computeZIPdelta | 0.000 | 0.000 | 0.001 | |
downloadPSet | 0 | 0 | 0 | |
downloadPertSig | 0.000 | 0.000 | 0.001 | |
drugDoseResponseCurve | 0.000 | 0.001 | 0.001 | |
drugPerturbationSig | 1.828 | 0.206 | 1.934 | |
drugSensitivitySig-PharmacoSet-method | 1.022 | 0.045 | 1.071 | |
effectToDose | 0 | 0 | 0 | |
filterNoisyCurves | 1.043 | 0.083 | 1.126 | |
fitTwowayZIP | 0.000 | 0.000 | 0.001 | |
geneDrugSensitivity | 0 | 0 | 0 | |
geneDrugSensitivityPBCorr | 0 | 0 | 0 | |
geneDrugSensitivityPCorr | 0 | 0 | 0 | |
gwc | 0.999 | 0.063 | 1.111 | |
hillCurve | 0.000 | 0.000 | 0.001 | |
intersectPSet | 1.239 | 0.102 | 1.258 | |
loeweCI | 0.000 | 0.000 | 0.001 | |
logLogisticRegression | 0.357 | 0.062 | 0.419 | |
mcc | 0.011 | 0.038 | 1.690 | |
plot.PharmacoSig | 2.714 | 0.652 | 1.663 | |
show-PharmacoSet-method | 1.016 | 0.093 | 1.109 | |
show-PharmacoSig-method | 1.018 | 0.246 | 1.261 | |
showSigAnnot-PharmacoSig-method | 0.950 | 0.061 | 1.009 | |
sub-PharmacoSet-ANY-ANY-ANY-method | 1.040 | 0.097 | 1.138 | |
subsetTo-PharmacoSet-method | 1.050 | 0.096 | 1.146 | |
summarizeMolecularProfiles-PharmacoSet-method | 0.109 | 0.044 | 0.153 | |
summarizeSensitivityProfiles-PharmacoSet-method | 0.056 | 0.013 | 0.069 | |
updateObject-PharmacoSet-method | 0.092 | 0.029 | 0.121 | |