| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 standR package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1952/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| standR 1.3.1 (landing page) Ning Liu
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: standR |
| Version: 1.3.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:standR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings standR_1.3.1.tar.gz |
| StartedAt: 2022-12-29 03:57:33 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 04:01:22 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 228.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: standR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:standR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings standR_1.3.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/standR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'standR/DESCRIPTION' ... OK
* this is package 'standR' version '1.3.1'
* 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 'standR' 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 ... 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
readGeoMx 9.03 2.50 10.59
findBestK 5.84 0.12 5.97
* 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: OK
standR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL standR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'standR' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for 'drawPCA' with signature '"DGEList"': no definition for class "DGEList" in method for 'drawPCA' with signature '"SpatialExperiment"': no definition for class "SpatialExperiment" in method for 'plotDR' with signature '"SpatialExperiment","ANY"': no definition for class "SpatialExperiment" in method for 'plotMDS' with signature '"DGEList","ANY","ANY","ANY"': no definition for class "DGEList" in method for 'plotMDS' with signature '"SpatialExperiment"': no definition for class "SpatialExperiment" in method for 'plotRLExpr' with signature '"DGEList","ANY"': no definition for class "DGEList" ** help *** installing help indices *** copying figures ** 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 (standR)
standR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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(standR)
>
> test_check("standR")
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
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: 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: 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
New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Loading required namespace: scater
Loading required package: scuttle
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:standR':
plotMDS
[ FAIL 0 | WARN 35 | SKIP 0 | PASS 107 ]
[ FAIL 0 | WARN 35 | SKIP 0 | PASS 107 ]
>
> proc.time()
user system elapsed
53.89 6.37 59.06
standR.Rcheck/standR-Ex.timings
| name | user | system | elapsed | |
| addPerROIQC | 2.54 | 0.12 | 2.67 | |
| computeClusterEvalStats | 0.66 | 0.07 | 0.72 | |
| dkd_spe_subset | 0.05 | 0.00 | 0.05 | |
| drawPCA | 0.30 | 0.00 | 0.29 | |
| findBestK | 5.84 | 0.12 | 5.97 | |
| findNCGs | 1.19 | 0.08 | 1.27 | |
| geomxBatchCorrection | 0.95 | 0.03 | 0.98 | |
| geomxNorm | 0.79 | 0.02 | 0.81 | |
| plotClusterEvalStats | 1.65 | 0.07 | 1.72 | |
| plotDR | 0.33 | 0.08 | 0.41 | |
| plotGeneQC | 0.86 | 0.03 | 0.89 | |
| plotMDS | 0.53 | 0.03 | 0.56 | |
| plotPCAbiplot | 0.31 | 0.00 | 0.32 | |
| plotPairPCA | 0.75 | 0.07 | 0.81 | |
| plotRLExpr | 1.13 | 0.02 | 1.14 | |
| plotROIQC | 0.72 | 0.00 | 0.72 | |
| plotSampleInfo | 0.59 | 0.03 | 0.63 | |
| plotScreePCA | 0.20 | 0.01 | 0.22 | |
| readGeoMx | 9.03 | 2.50 | 10.59 | |
| readGeoMxFromDGE | 0.21 | 0.00 | 0.20 | |