Benjamin Haibe-Kains
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CoreGx |
| git_branch: master |
| git_last_commit: b78b5a5 |
| git_last_commit_date: 2021-10-26 12:59:39 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:16 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 402/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoreGx 1.7.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CoreGx |
| Version: 1.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoreGx_1.7.0.tar.gz |
| StartedAt: 2022-03-17 18:48:39 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:53:04 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 265.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoreGx.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoreGx_1.7.0.tar.gz
###
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##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '1.7.0'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.paste_slashes: no visible binding for global variable '..'
.rebuildInfo: no visible global function definition for 'patterns'
.rebuildInfo: no visible binding for global variable '..keepCols'
.rebuildInfo: no visible binding for global variable 'drugid'
.rebuildInfo: no visible binding for global variable 'drug1id'
.rebuildInfo: no visible binding for global variable 'drug_uid'
.rebuildInfo: no visible binding for global variable '..rowIDcols'
.rebuildInfo: no visible binding for global variable 'cell_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 'cell_uid'
.rebuildProfiles: no visible binding for global variable 'drug_uid'
.rebuildProfiles: no visible binding for global variable 'exp_id'
.rebuildRaw: no visible binding for global variable '.NATURAL'
.rebuildRaw: no visible binding for global variable 'cellid'
.rebuildRaw: no visible binding for global variable 'exp_id'
.rebuildRaw: no visible binding for global variable 'drug1id'
.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 '.drugCombo'
.rebuildSensNumber: no visible binding for global variable '.cellCombo'
.sensitivityToLongTable: no visible binding for global variable 'dose'
.sensitivityToLongTable: no visible binding for global variable
'viability'
.sensitivityToLongTable: no visible binding for global variable
'replicate_id'
.summarizePerturbationNumbers: no visible global function definition
for 'drugInfo'
.summarizeSensitivityNumbers: no visible global function definition for
'drugInfo'
assay<-,LongTable-character: no visible binding for global variable
'..missingRowCols'
assay<-,LongTable-character: no visible binding for global variable
'..missingColCols'
coerce,SummarizedExperiment-data.table: no visible binding for global
variable '.sample'
coerce,SummarizedExperiment-data.table: no visible binding for global
variable '.feature'
colData<-,LongTable-ANY: no visible binding for global variable
'.NATURAL'
colData<-,LongTable-ANY: no visible binding for global variable
'.colnames'
metaConstruct,LongTableDataMapper: no visible binding for global
variable '..rowIDs'
metaConstruct,LongTableDataMapper: no visible binding for global
variable '..colIDs'
rowData<-,LongTable: no visible binding for global variable '.NATURAL'
rowData<-,LongTable: no visible binding for global variable '.rownames'
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
'cell_uid'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
'rn'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
'row_id'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
'col_id'
sensitivitySlot<-,CoreSet-list_or_LongTable: no visible binding for
global variable 'funContext'
updateObject,CoreSet: no visible global function definition for
'isValid'
Undefined global functions or variables:
.. ..colIDcols ..colIDs ..keepCols ..missingColCols ..missingRowCols
..rowIDcols ..rowIDs .NATURAL .cellCombo .colnames .drugCombo
.feature .rownames .sample V1 V2 cell_uid cellid col_id col_ids dose
drug1id drugInfo drug_uid drugid exp_id funContext isValid patterns
replicate_id rn row_id row_ids viability
* 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 ... 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 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 1.91 0.03 17.24
gwc 0.72 0.00 8.52
cosinePerm 0.70 0.00 8.08
connectivityScore 0.61 0.00 11.91
mcc 0.58 0.01 13.42
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck/00check.log'
for details.
CoreGx.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CoreGx
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CoreGx' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for 'colnames' from package 'base' in package 'CoreGx'
Creating a generic function for 'rownames' from package 'base' in package 'CoreGx'
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CoreGx'
finding HTML links ... done
CoreSet-accessors html
CoreSet-class html
CoreSet-utils html
CoreSet html
CoreSet2 html
Create html
DataMapper-accessors html
DataMapper-class html
LongTable-accessors html
LongTable-class html
LongTable html
LongTableDataMapper-accessors html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CoreGx/00new/CoreGx/help/assayMap+2CLongTableDataMapper+2CList-method.html
LongTableDataMapper-class html
LongTableDataMapper html
TREDataMapper-class html
TREDataMapper html
TreatmentResponseExperiment-class html
TreatmentResponseExperiment html
amcc html
as html
as.long.table html
assayCols html
buildLongTable html
callingWaterfall html
cash-LongTable-method html
cash-set-LongTable-method html
checkColumnCardinality html
checkCsetStructure html
clevelandSmall_cSet html
colIDs html
colMeta html
connectivityScore html
cosinePerm html
dot- html
dot-assayToBumpyMatrix html
dot-convertCSetMolecularProfilesToSE html
dot-distancePointLine html
dot-distancePointSegment html
dot-intersectList html
dot-longTableToSummarizedExperiment html
dot-sensitivityToLongTable html
dot-symSetDiffList html
dot-unionList html
drugSensitivitySig html
exampleDataMapper html
getIntern html
guessMapping-LongTableDataMapper-method
html
guessMapping html
gwc html
idCols-LongTable-method html
idCols html
is.items html
lapply-MultiAssayExperiment-method html
list_or_LongTable-class html
mcc html
merckLongTable html
metaConstruct html
metadata-LongTable-method html
metadata-set-LongTable-method html
reindex-LongTable-method html
reindex html
rowIDs html
rowMeta html
sensitivityInfo-set html
sensitivityInfo html
sensitivityMeasures-set html
sensitivityMeasures html
sensitivityProfiles-set html
sensitivityProfiles html
sensitivityRaw-set html
sensitivityRaw html
sensitivitySlotToLongTable html
show-CoreSet-method html
show-LongTable-method html
showSigAnnot html
sub-LongTable-ANY-ANY-ANY-method html
sub-subset-LongTable-ANY-ANY-method html
subset-LongTable-method html
subsetTo html
summarizeMolecularProfiles html
summarizeSensitivityProfiles html
updateCellId html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'LiquidAssociation' is missing or broken
done
CoreGx.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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, 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
7.54 0.70 8.23
CoreGx.Rcheck/CoreGx-Ex.timings
| name | user | system | elapsed | |
| CoreSet-accessors | 1.09 | 0.11 | 1.20 | |
| CoreSet-utils | 0.41 | 0.00 | 0.41 | |
| CoreSet | 0.03 | 0.00 | 0.03 | |
| CoreSet2 | 0.03 | 0.00 | 0.03 | |
| Create | 0.14 | 0.00 | 0.14 | |
| LongTable-accessors | 0 | 0 | 0 | |
| LongTable-class | 0.28 | 0.01 | 0.30 | |
| LongTable | 0.02 | 0.00 | 0.02 | |
| LongTableDataMapper-accessors | 0 | 0 | 0 | |
| LongTableDataMapper-class | 0.01 | 0.00 | 0.01 | |
| LongTableDataMapper | 0 | 0 | 0 | |
| amcc | 1.91 | 0.03 | 17.24 | |
| as | 0.51 | 0.13 | 0.62 | |
| as.long.table | 0.11 | 0.00 | 0.13 | |
| assayCols | 0 | 0 | 0 | |
| buildLongTable | 0 | 0 | 0 | |
| callingWaterfall | 0 | 0 | 0 | |
| cash-LongTable-method | 0.02 | 0.00 | 0.01 | |
| cash-set-LongTable-method | 0.03 | 0.00 | 0.03 | |
| checkColumnCardinality | 0 | 0 | 0 | |
| checkCsetStructure | 0.03 | 0.00 | 0.03 | |
| colIDs | 0 | 0 | 0 | |
| colMeta | 0 | 0 | 0 | |
| connectivityScore | 0.61 | 0.00 | 11.91 | |
| cosinePerm | 0.70 | 0.00 | 8.08 | |
| dot- | 0 | 0 | 0 | |
| dot-distancePointLine | 0 | 0 | 0 | |
| dot-distancePointSegment | 0 | 0 | 0 | |
| dot-intersectList | 0 | 0 | 0 | |
| dot-symSetDiffList | 0 | 0 | 0 | |
| dot-unionList | 0 | 0 | 0 | |
| getIntern | 0 | 0 | 0 | |
| guessMapping-LongTableDataMapper-method | 0.02 | 0.00 | 0.01 | |
| gwc | 0.72 | 0.00 | 8.52 | |
| idCols-LongTable-method | 0 | 0 | 0 | |
| idCols | 0 | 0 | 0 | |
| is.items | 0 | 0 | 0 | |
| mcc | 0.58 | 0.01 | 13.42 | |
| metaConstruct | 0.12 | 0.00 | 0.13 | |
| 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 | 0.01 | |
| sensitivityProfiles | 0 | 0 | 0 | |
| sensitivityRaw | 0 | 0 | 0 | |
| sensitivitySlotToLongTable | 0 | 0 | 0 | |
| show-CoreSet-method | 0.01 | 0.00 | 0.02 | |
| show-LongTable-method | 0.03 | 0.00 | 0.03 | |
| showSigAnnot | 0 | 0 | 0 | |
| sub-LongTable-ANY-ANY-ANY-method | 0.3 | 0.0 | 0.3 | |
| sub-subset-LongTable-ANY-ANY-method | 0.03 | 0.00 | 0.03 | |
| subset-LongTable-method | 0.19 | 0.00 | 0.19 | |
| summarizeMolecularProfiles | 0 | 0 | 0 | |
| summarizeSensitivityProfiles | 0 | 0 | 0 | |
| updateCellId | 0.11 | 0.00 | 0.10 | |