Catalina Vallejos
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/BASiCS |
| git_branch: RELEASE_3_16 |
| git_last_commit: 6de1264 |
| git_last_commit_date: 2023-01-19 11:14:20 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:25 -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 BASiCS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.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 118/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.10.5 (landing page) Catalina Vallejos
| 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: BASiCS |
| Version: 2.10.5 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BASiCS.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BASiCS_2.10.5.tar.gz |
| StartedAt: 2023-04-10 23:04:27 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:12:16 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 469.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BASiCS.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BASiCS_2.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BASiCS.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 'BASiCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BASiCS' version '2.10.5'
* 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 'BASiCS' 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/BASiCS/libs/x64/BASiCS.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BASiCS_MCMC 7.66 0.09 7.81
BASiCS_TestDE 7.02 0.08 7.11
BASiCS_DivideAndConquer 2.48 0.08 17.91
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/BASiCS.Rcheck/00check.log'
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'BASiCS' ... ** using staged installation ** libs g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BASiCS.cpp -o BASiCS.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS.o RcppExports.o -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/libs/x64 ** 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 (BASiCS)
BASiCS.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(BASiCS)
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
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
>
> test_check("BASiCS")
Starting 2 test processes
[ FAIL 0 | WARN 248 | SKIP 0 | PASS 447 ]
[ FAIL 0 | WARN 248 | SKIP 0 | PASS 447 ]
>
> proc.time()
user system elapsed
18.14 1.01 166.67
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 2.59 | 0.14 | 2.74 | |
| BASiCS_Chain | 4.15 | 0.03 | 4.17 | |
| BASiCS_CorrectOffset | 0.02 | 0.02 | 0.03 | |
| BASiCS_DenoisedCounts | 2.70 | 0.05 | 2.75 | |
| BASiCS_DenoisedRates | 2.72 | 0.03 | 2.75 | |
| BASiCS_DetectVG | 0.73 | 0.09 | 0.83 | |
| BASiCS_DiagHist | 0.96 | 0.08 | 1.03 | |
| BASiCS_DiagPlot | 0.61 | 0.01 | 0.63 | |
| BASiCS_DivideAndConquer | 2.48 | 0.08 | 17.91 | |
| BASiCS_Draw | 0.50 | 0.02 | 0.53 | |
| BASiCS_EffectiveSize | 0.2 | 0.0 | 0.2 | |
| BASiCS_Filter | 0.00 | 0.01 | 0.02 | |
| BASiCS_LoadChain | 2.14 | 0.02 | 2.15 | |
| BASiCS_MCMC | 7.66 | 0.09 | 7.81 | |
| BASiCS_MockSCE | 0.36 | 0.05 | 0.41 | |
| BASiCS_PlotDE | 3.40 | 0.05 | 3.43 | |
| BASiCS_PlotOffset | 1.07 | 0.04 | 1.13 | |
| BASiCS_PlotVG | 0.35 | 0.02 | 0.36 | |
| BASiCS_PriorParam | 0.31 | 0.00 | 0.31 | |
| BASiCS_ShowFit | 0.22 | 0.03 | 0.25 | |
| BASiCS_Sim | 0.87 | 0.00 | 0.88 | |
| BASiCS_Summary-methods | 0 | 0 | 0 | |
| BASiCS_Summary | 2.25 | 0.00 | 2.25 | |
| BASiCS_TestDE | 7.02 | 0.08 | 7.11 | |
| BASiCS_VarThresholdSearchHVG_LVG | 1.76 | 0.01 | 1.78 | |
| BASiCS_VarianceDecomp | 0.25 | 0.00 | 0.25 | |
| Summary-BASiCS_Chain-method | 0.05 | 0.02 | 0.06 | |
| dim-BASiCS_Chain-method | 0.02 | 0.00 | 0.02 | |
| dimnames-BASiCS_Chain-method | 0.01 | 0.00 | 0.01 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.21 | 0.06 | 1.45 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.14 | 0.08 | 0.22 | |
| makeExampleBASiCS_Data | 0.37 | 0.00 | 0.38 | |
| newBASiCS_Chain | 4.53 | 0.08 | 4.61 | |
| plot-BASiCS_Chain-method | 0.19 | 0.05 | 0.25 | |
| plot-BASiCS_Summary-method | 0.16 | 0.04 | 0.22 | |
| show-BASiCS_ResultDE-method | 0.15 | 0.05 | 0.21 | |
| show-BASiCS_ResultVG-method | 0.11 | 0.08 | 0.22 | |
| show-BASiCS_ResultsDE-method | 0.19 | 0.04 | 0.25 | |
| subset-BASiCS_Chain-method | 1.09 | 0.02 | 1.11 | |