Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:29 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the CoreGx package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 417/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CoreGx 2.2.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: CoreGx |
Version: 2.2.0 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CoreGx_2.2.0.tar.gz |
StartedAt: 2023-04-11 00:22:30 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 00:30:38 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 488.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CoreGx.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CoreGx_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CoreGx.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CoreGx/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CoreGx' version '2.2.0' * 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 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 R 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 ... NOTE Found the following apparent S3 methods exported but not registered: subset.immutable See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .checkForIdColumn: no visible binding for global variable 'col_col' .meshEval2: no visible binding for global variable 'n' .meshEval2: no visible binding for global variable 'family' .rebuildInfo: no visible global function definition for 'patterns' .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 'row_ids' .rebuildRaw: no visible binding for global variable 'col_ids' .rebuildRaw: no visible binding for global variable 'dose' .rebuildRaw: no visible global function definition for 'patterns' .rebuildSensNumber: no visible global function definition for 'patterns' .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' CoreSet: no visible global function definition for '.checkForIdColumns' 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 .checkForIdColumns .colKey .feature .rowKey .rownames .sample .sampleCombo .treatmentCombo N V1 V2 cell col_col col_ids dose drug exp_id family funContext gc/sec group_id isValid itr/sec median_sec mem_alloc n nthread patterns replicate_id rn row_ids 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 S3 methods shown with full name in documentation object 'setOps-immutable': '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 8 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 amcc 2.20 0.03 25.06 cosinePerm 0.84 0.02 11.84 mcc 0.75 0.02 12.83 gwc 0.72 0.03 11.45 connectivityScore 0.72 0.01 11.22 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See 'F:/biocbuild/bbs-3.16-bioc/meat/CoreGx.Rcheck/00check.log' for details.
CoreGx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CoreGx ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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, setdiff, sort, 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 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 > > 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% | | | 0% | |=================================== | 50% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 131 ] > > proc.time() user system elapsed 145.17 2.26 188.01
CoreGx.Rcheck/CoreGx-Ex.timings
name | user | system | elapsed | |
CoreSet-accessors | 1.00 | 0.09 | 1.14 | |
CoreSet-utils | 0.41 | 0.00 | 0.40 | |
CoreSet | 0.01 | 0.00 | 0.02 | |
CoreSet2 | 0.02 | 0.00 | 0.01 | |
LongTable-accessors | 0 | 0 | 0 | |
LongTable-class | 1.17 | 0.04 | 1.30 | |
LongTable | 0 | 0 | 0 | |
LongTableDataMapper-accessors | 0.00 | 0.02 | 0.01 | |
LongTableDataMapper-class | 0 | 0 | 0 | |
LongTableDataMapper | 0.00 | 0.02 | 0.02 | |
TREDataMapper-accessors | 0.06 | 0.00 | 0.06 | |
amcc | 2.20 | 0.03 | 25.06 | |
as | 0.57 | 0.20 | 0.83 | |
as.long.table | 0.08 | 0.02 | 0.10 | |
assayCols | 0 | 0 | 0 | |
assayIndex | 0 | 0 | 0 | |
assayKeys | 0 | 0 | 0 | |
assignment-immutable | 0 | 0 | 0 | |
buildComboProfiles-LongTable-method | 0 | 0 | 0 | |
buildComboProfiles | 0 | 0 | 0 | |
buildLongTable-list-method | 0 | 0 | 0 | |
buildLongTable | 0 | 0 | 0 | |
callingWaterfall | 0 | 0 | 0 | |
cash-LongTable-method | 0.01 | 0.00 | 0.02 | |
cash-set-LongTable-method | 0.08 | 0.00 | 0.08 | |
checkColumnCardinality | 0 | 0 | 0 | |
checkCsetStructure | 0.03 | 0.00 | 0.03 | |
colIDs | 0 | 0 | 0 | |
colMeta | 0 | 0 | 0 | |
connectivityScore | 0.72 | 0.01 | 11.22 | |
cosinePerm | 0.84 | 0.02 | 11.84 | |
dot- | 0 | 0 | 0 | |
dot-distancePointLine | 0 | 0 | 0 | |
dot-distancePointSegment | 0 | 0 | 0 | |
dot-fitCurve2 | 0 | 0 | 0 | |
dot-intersectList | 0 | 0 | 0 | |
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 | 0.01 | 0.00 | 0.01 | |
guessMapping | 0 | 0 | 0 | |
gwc | 0.72 | 0.03 | 11.45 | |
idCols | 0 | 0 | 0 | |
immutable | 0.02 | 0.00 | 0.02 | |
is.items | 0 | 0 | 0 | |
mcc | 0.75 | 0.02 | 12.83 | |
mergeAssays | 0 | 0 | 0 | |
metaConstruct | 0.06 | 0.01 | 0.08 | |
mutable | 0 | 0 | 0 | |
optimizeCoreGx | 0 | 0 | 0 | |
reindex | 0 | 0 | 0 | |
rowIDs | 0 | 0 | 0 | |
rowMeta | 0 | 0 | 0 | |
sensitivityInfo-set | 0 | 0 | 0 | |
sensitivityInfo | 0 | 0 | 0 | |
sensitivityMeasures-set | 0 | 0 | 0 | |
sensitivityMeasures | 0.02 | 0.00 | 0.02 | |
sensitivityProfiles | 0 | 0 | 0 | |
sensitivityRaw | 0 | 0 | 0 | |
sensitivitySlotToLongTable | 0 | 0 | 0 | |
setOps-immutable | 0 | 0 | 0 | |
show-CoreSet-method | 0.01 | 0.00 | 0.01 | |
show-LongTable-method | 0 | 0 | 0 | |
showSigAnnot | 0 | 0 | 0 | |
sub-LongTable-ANY-ANY-ANY-method | 0.28 | 0.00 | 0.28 | |
sub-subset-LongTable-ANY-ANY-method | 0.07 | 0.01 | 0.08 | |
subset-LongTable-method | 0.18 | 0.00 | 0.19 | |
subsetTo | 0 | 0 | 0 | |
summarizeMolecularProfiles | 0 | 0 | 0 | |
summarizeSensitivityProfiles | 0 | 0 | 0 | |
updateSampleId | 0.13 | 0.02 | 0.14 | |
updateTreatmentId | 0.01 | 0.00 | 0.02 | |