Benjamin Haibe-Kains
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/PharmacoGx |
| git_branch: master |
| git_last_commit: f3d1fbf |
| git_last_commit_date: 2021-10-26 12:29:36 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:17 -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 PharmacoGx package: - Please 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 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 1412/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PharmacoGx 2.7.0 (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: PharmacoGx |
| Version: 2.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PharmacoGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PharmacoGx_2.7.0.tar.gz |
| StartedAt: 2022-03-17 19:51:25 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:57:02 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 337.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PharmacoGx.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:PharmacoGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PharmacoGx_2.7.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PharmacoGx.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 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '2.7.0'
* 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 'PharmacoGx' 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 ... OK
* 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 2251 marked UTF-8 strings
* 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 1.61 0.00 22.78
gwc 1.35 0.04 10.99
connectivityScore 0.52 0.00 7.79
mcc 0.48 0.04 9.75
cosinePerm 0.45 0.00 11.31
* 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.
PharmacoGx.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PharmacoGx
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PharmacoGx' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PharmacoGx'
finding HTML links ... done
CCLEsmall html
CMAPsmall html
GDSCsmall html
HDAC_genes html
PharmacoSet-accessors html
PharmacoSet-class html
PharmacoSet-utils html
PharmacoSet html
PharmacoSet2 html
PharmacoSig html
amcc html
availablePSets html
callingWaterfall html
checkPsetStructure html
computeABC html
computeAUC html
computeAmax html
computeICn html
computeSlope html
connectivityScore html
cosinePerm html
dim-PharmacoSet-method html
dot-summarizeSensProfiles html
downloadPSet html
downloadPertSig html
drugDoseResponseCurve html
drugInfo-set html
drugInfo html
drugNames-set html
drugNames html
drugPerturbationSig html
drugSensitivitySig-PharmacoSet-method html
filterNoisyCurves html
geneDrugSensitivity html
gwc html
intersectPSet html
logLogisticRegression html
mcc html
plot.PharmacoSig html
show-PharmacoSet-method html
show-PharmacoSig-method html
showSigAnnot-PharmacoSig-method html
sub-PharmacoSet-ANY-ANY-ANY-method html
subsetTo-PharmacoSet-method html
summarizeMolecularProfiles-PharmacoSet-method
html
summarizeSensitivityProfiles-PharmacoSet-method
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 (PharmacoGx)
Making 'packages.html' ... done
PharmacoGx.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.
> Sys.unsetenv("R_TESTS")
>
> library(testthat)
> library(PharmacoGx)
Loading required package: 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
Attaching package: 'PharmacoGx'
The following objects are masked from 'package:CoreGx':
.parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc
>
> test_check("PharmacoGx")
[1] NA 3
[1] 1 2 Inf
[1] NA 3
[1] 1 2 Inf
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[1] 1 1 -1
[1] 0
[1] 0
[,1] [,2] [,3]
lower_bounds 0 0 0
upper_bounds 1 1 -1
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[ FAIL 0 | WARN 0 | SKIP 1 | PASS 129 ]
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 129 ]
>
> proc.time()
user system elapsed
47.93 1.20 49.12
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
| name | user | system | elapsed | |
| PharmacoSet-accessors | 3.34 | 1.29 | 4.67 | |
| PharmacoSet-utils | 0.97 | 0.08 | 1.05 | |
| PharmacoSet | 0 | 0 | 0 | |
| PharmacoSet2 | 0.72 | 0.02 | 0.73 | |
| amcc | 1.61 | 0.00 | 22.78 | |
| availablePSets | 0 | 0 | 0 | |
| callingWaterfall | 0 | 0 | 0 | |
| checkPsetStructure | 0.70 | 0.01 | 0.72 | |
| computeABC | 0.50 | 0.13 | 0.62 | |
| computeAUC | 0.32 | 0.00 | 0.32 | |
| computeAmax | 0.31 | 0.00 | 0.31 | |
| computeICn | 0.61 | 0.00 | 0.61 | |
| computeSlope | 0.01 | 0.00 | 0.01 | |
| connectivityScore | 0.52 | 0.00 | 7.79 | |
| cosinePerm | 0.45 | 0.00 | 11.31 | |
| downloadPSet | 0 | 0 | 0 | |
| downloadPertSig | 0 | 0 | 0 | |
| drugDoseResponseCurve | 0 | 0 | 0 | |
| drugNames-set | 0.89 | 0.04 | 0.94 | |
| drugNames | 0.91 | 0.08 | 0.98 | |
| drugPerturbationSig | 1.56 | 0.03 | 1.59 | |
| drugSensitivitySig-PharmacoSet-method | 0.78 | 0.00 | 0.78 | |
| filterNoisyCurves | 0.48 | 0.00 | 0.50 | |
| gwc | 1.35 | 0.04 | 10.99 | |
| intersectPSet | 0.79 | 0.03 | 0.82 | |
| logLogisticRegression | 0.32 | 0.00 | 0.32 | |
| mcc | 0.48 | 0.04 | 9.75 | |
| plot.PharmacoSig | 0.91 | 0.05 | 0.95 | |
| show-PharmacoSet-method | 0.69 | 0.06 | 0.75 | |
| show-PharmacoSig-method | 0.70 | 0.03 | 0.73 | |
| showSigAnnot-PharmacoSig-method | 0.70 | 0.02 | 0.72 | |
| sub-PharmacoSet-ANY-ANY-ANY-method | 0.72 | 0.02 | 0.74 | |
| subsetTo-PharmacoSet-method | 0.72 | 0.04 | 0.76 | |
| summarizeMolecularProfiles-PharmacoSet-method | 0.11 | 0.00 | 0.11 | |
| summarizeSensitivityProfiles-PharmacoSet-method | 0.03 | 0.02 | 0.05 | |