Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 437/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CoreGx 2.10.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 | |||||||||
To the developers/maintainers of the CoreGx package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoreGx.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: CoreGx |
Version: 2.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoreGx_2.10.0.tar.gz |
StartedAt: 2024-12-20 15:41:19 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 15:47:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 374.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CoreGx.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoreGx_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoreGx.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CoreGx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CoreGx’ version ‘2.10.0’ * 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 ‘CoreGx’ can be installed ... OK * 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 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: ‘.LongTable’ ‘.parseToRoxygen’ ‘.sensitivityToTRE’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .meshEval2: no visible binding for global variable ‘n’ .meshEval2: no visible binding for global variable ‘family’ .rebuildInfo: no visible binding for global variable ‘..keepCols’ .rebuildInfo: no visible binding for global variable ‘replicate_id’ .rebuildInfo: no visible binding for global variable ‘treatment1id’ .rebuildInfo: no visible binding for global variable ‘sampleid’ .rebuildInfo: no visible binding for global variable ‘treatmentid’ .rebuildInfo: no visible binding for global variable ‘treatment_uid’ .rebuildInfo: no visible binding for global variable ‘..rowIDcols’ .rebuildInfo: no visible binding for global variable ‘sample_uid’ .rebuildInfo: no visible binding for global variable ‘..colIDcols’ .rebuildInfo: no visible binding for global variable ‘exp_id’ .rebuildProfiles: no visible binding for global variable ‘treatment_uid’ .rebuildProfiles: no visible binding for global variable ‘sample_uid’ .rebuildProfiles: no visible binding for global variable ‘exp_id’ .rebuildProfiles: no visible binding for global variable ‘N’ .rebuildRaw: no visible binding for global variable ‘.NATURAL’ .rebuildRaw: no visible binding for global variable ‘sampleid’ .rebuildRaw: no visible binding for global variable ‘exp_id’ .rebuildRaw: no visible binding for global variable ‘treatment1id’ .rebuildRaw: no visible binding for global variable ‘dose’ .rebuildSensNumber: no visible binding for global variable ‘.treatmentCombo’ .rebuildSensNumber: no visible binding for global variable ‘.sampleCombo’ .sensitivityToTRE: no visible binding for global variable ‘dose’ .sensitivityToTRE: no visible binding for global variable ‘viability’ .sensitivityToTRE: no visible binding for global variable ‘replicate_id’ .sensitivityToTRE: no visible binding for global variable ‘rn’ .sensitivityToTRE: no visible binding for global variable ‘treatmentid’ .sensitivityToTRE: no visible binding for global variable ‘sampleid’ .update_dimData: no visible binding for global variable ‘N’ .update_dimData: no visible binding for global variable ‘.NATURAL’ .update_dimData: no visible binding for global variable ‘.rownames’ CoreSet: no visible binding for global variable ‘cell’ CoreSet: no visible binding for global variable ‘drug’ aggregate2: no visible binding for global variable ‘group_id’ aggregate2: no visible binding for global variable ‘split_id’ cardinality: no visible binding for global variable ‘N’ checkColumnCardinality: no visible binding for global variable ‘N’ optimizeCoreGx: no visible binding for global variable ‘nthread’ optimizeCoreGx: no visible binding for global variable ‘total_time’ optimizeCoreGx: no visible binding for global variable ‘mem_alloc’ optimizeCoreGx: no visible binding for global variable ‘itr/sec’ optimizeCoreGx: no visible binding for global variable ‘gc/sec’ optimizeCoreGx: no visible binding for global variable ‘median_sec’ optimizeCoreGx: no visible binding for global variable ‘N’ buildComboProfiles,LongTable: no visible binding for global variable ‘treatment2dose’ buildComboProfiles,LongTable: no visible binding for global variable ‘treatment1dose’ coerce,SummarizedExperiment-data.table: no visible binding for global variable ‘.sample’ coerce,SummarizedExperiment-data.table: no visible binding for global variable ‘.feature’ reindex,LongTable: no visible binding for global variable ‘.rowKey’ reindex,LongTable: no visible binding for global variable ‘.colKey’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘V2’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘V1’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘rn’ treatmentResponse<-,CoreSet-list_OR_LongTable: no visible binding for global variable ‘funContext’ updateObject,CoreSet: no visible global function definition for ‘isValid’ updateObject,LongTable: no visible global function definition for ‘isValid’ Undefined global functions or variables: ..colIDcols ..keepCols ..rowIDcols .NATURAL .colKey .feature .rowKey .rownames .sample .sampleCombo .treatmentCombo N V1 V2 cell dose drug exp_id family funContext gc/sec group_id isValid itr/sec median_sec mem_alloc n nthread replicate_id rn sample_uid sampleid split_id total_time treatment1dose treatment1id treatment2dose treatment_uid treatmentid viability Consider adding importFrom("stats", "family") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'LongTable-class.Rd': ‘`x`’ ‘`i`’ Documented arguments not in \usage in Rd file 'assays-LongTableDataMapper-method.Rd': ‘withDimNames’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. S3 methods shown with full name in Rd file 'setOps-immutable.Rd': ‘subset.immutable’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 99 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed metaConstruct 9.847 0.607 8.875 as 6.234 0.795 4.975 as.long.table 5.297 0.149 4.422 * 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-3.20-bioc/meat/CoreGx.Rcheck/00check.log’ for details.
CoreGx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoreGx ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CoreGx’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CoreGx)
CoreGx.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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. > library(testthat) > library(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, saveRDS, 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 > > test_check("CoreGx") Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second | | | 0% | |=================================== | 50% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-LongTable-accessors.R:13:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ] > > proc.time() user system elapsed 75.897 2.777 71.520
CoreGx.Rcheck/CoreGx-Ex.timings
name | user | system | elapsed | |
CoreSet-accessors | 2.593 | 0.095 | 2.123 | |
CoreSet-utils | 0.458 | 0.014 | 0.400 | |
CoreSet | 0.025 | 0.004 | 0.029 | |
CoreSet2 | 0.024 | 0.004 | 0.029 | |
LongTable-accessors | 0.001 | 0.003 | 0.004 | |
LongTable-class | 1.158 | 0.090 | 0.697 | |
LongTable | 0 | 0 | 0 | |
LongTableDataMapper-accessors | 0.005 | 0.000 | 0.003 | |
LongTableDataMapper-class | 0.009 | 0.001 | 0.006 | |
LongTableDataMapper | 0.012 | 0.003 | 0.008 | |
TREDataMapper-accessors | 0.133 | 0.007 | 0.073 | |
amcc | 3.562 | 0.104 | 4.402 | |
as | 6.234 | 0.795 | 4.975 | |
as.long.table | 5.297 | 0.149 | 4.422 | |
assayCols | 0.001 | 0.000 | 0.000 | |
assayIndex | 0.000 | 0.001 | 0.000 | |
assayKeys | 0 | 0 | 0 | |
assignment-immutable | 0.005 | 0.002 | 0.003 | |
buildComboProfiles-LongTable-method | 0.001 | 0.000 | 0.000 | |
buildComboProfiles | 0.001 | 0.000 | 0.001 | |
buildLongTable-list-method | 0.000 | 0.001 | 0.001 | |
buildLongTable | 0 | 0 | 0 | |
callingWaterfall | 0 | 0 | 0 | |
cash-LongTable-method | 0.035 | 0.003 | 0.020 | |
cash-set-LongTable-method | 0.143 | 0.010 | 0.081 | |
checkColumnCardinality | 0.006 | 0.001 | 0.003 | |
checkCsetStructure | 0.062 | 0.005 | 0.035 | |
colIDs | 0.001 | 0.000 | 0.001 | |
colMeta | 0 | 0 | 0 | |
connectivityScore | 0.164 | 0.092 | 0.134 | |
cosinePerm | 0.062 | 0.075 | 0.110 | |
dot- | 0.000 | 0.000 | 0.001 | |
dot-distancePointLine | 0 | 0 | 0 | |
dot-distancePointSegment | 0.000 | 0.001 | 0.001 | |
dot-fitCurve2 | 0.000 | 0.001 | 0.000 | |
dot-intersectList | 0.000 | 0.000 | 0.001 | |
dot-symSetDiffList | 0 | 0 | 0 | |
dot-unionList | 0 | 0 | 0 | |
endoaggregate | 0 | 0 | 0 | |
getIntern-set | 0 | 0 | 0 | |
getIntern | 0 | 0 | 0 | |
guessMapping-LongTableDataMapper-method | 0.015 | 0.009 | 0.016 | |
guessMapping | 0 | 0 | 0 | |
gwc | 0.241 | 0.127 | 0.197 | |
idCols | 0 | 0 | 0 | |
immutable | 0.002 | 0.005 | 0.007 | |
is.items | 0.001 | 0.001 | 0.001 | |
mcc | 0.011 | 0.026 | 1.606 | |
mergeAssays | 0 | 0 | 0 | |
metaConstruct | 9.847 | 0.607 | 8.875 | |
mutable | 0.001 | 0.000 | 0.001 | |
optimizeCoreGx | 0 | 0 | 0 | |
reindex | 0.000 | 0.001 | 0.000 | |
rowIDs | 0.001 | 0.000 | 0.001 | |
rowMeta | 0.000 | 0.001 | 0.001 | |
sensitivityInfo-set | 0 | 0 | 0 | |
sensitivityInfo | 0.000 | 0.001 | 0.000 | |
sensitivityMeasures-set | 0 | 0 | 0 | |
sensitivityMeasures | 0.018 | 0.002 | 0.018 | |
sensitivityProfiles | 0.000 | 0.000 | 0.001 | |
sensitivityRaw | 0 | 0 | 0 | |
sensitivitySlotToLongTable | 0 | 0 | 0 | |
setOps-immutable | 0.001 | 0.000 | 0.000 | |
show-CoreSet-method | 0.016 | 0.002 | 0.010 | |
show-LongTable-method | 0.009 | 0.001 | 0.005 | |
showSigAnnot | 0 | 0 | 0 | |
sub-LongTable-ANY-ANY-ANY-method | 0.523 | 0.042 | 0.289 | |
sub-subset-LongTable-ANY-ANY-method | 0.143 | 0.013 | 0.081 | |
subset-LongTable-method | 0.289 | 0.032 | 0.167 | |
subsetTo | 0 | 0 | 0 | |
summarizeMolecularProfiles | 0.001 | 0.000 | 0.000 | |
summarizeSensitivityProfiles | 0 | 0 | 0 | |
updateSampleId | 0.247 | 0.026 | 0.142 | |
updateTreatmentId | 0.017 | 0.002 | 0.010 | |