Alan O'Callaghan
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BASiCS |
| git_branch: master |
| git_last_commit: 94eb264 |
| git_last_commit_date: 2022-02-22 18:54:56 -0400 (Tue, 22 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:59 -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 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? 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 115/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.7.5 (landing page) Alan O'Callaghan
| 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: BASiCS |
| Version: 2.7.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BASiCS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BASiCS_2.7.5.tar.gz |
| StartedAt: 2022-03-17 18:29:39 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:36:30 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 410.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.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:BASiCS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BASiCS_2.7.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BASiCS.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 'BASiCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BASiCS' version '2.7.5'
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/BASiCS/libs/x64/BASiCS.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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_TestDE 6.72 0.03 6.75
BASiCS_MCMC 5.66 0.03 5.69
BASiCS_DivideAndConquer 1.86 0.02 15.03
* 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/BASiCS.Rcheck/00check.log'
for details.
BASiCS.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BASiCS
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BASiCS' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c BASiCS.cpp -o BASiCS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS.o RcppExports.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
converting help for package 'BASiCS'
finding HTML links ... done
BASiCS-defunct html
BASiCS_Chain-methods html
BASiCS_Chain html
BASiCS_CorrectOffset html
BASiCS_DenoisedCounts html
finding level-2 HTML links ... done
BASiCS_DenoisedRates html
BASiCS_DetectVG html
BASiCS_DiagHist html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_diagHist.html
BASiCS_DiagPlot html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_diagPlot.html
BASiCS_DivideAndConquer html
BASiCS_Draw html
BASiCS_EffectiveSize html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_effectiveSize.html
BASiCS_Filter html
BASiCS_LoadChain html
BASiCS_MCMC html
BASiCS_MockSCE html
BASiCS_PlotDE html
BASiCS_PlotOffset html
BASiCS_PlotVG html
BASiCS_PriorParam html
BASiCS_Result html
BASiCS_ResultDE html
BASiCS_ResultVG html
BASiCS_ResultsDE html
BASiCS_ShowFit html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_showFit.html
BASiCS_Sim html
BASiCS_Summary-methods html
BASiCS_Summary html
BASiCS_TestDE html
BASiCS_VarThresholdSearchHVG_LVG html
BASiCS_VarianceDecomp html
ChainRNA html
ChainRNAReg html
ChainSC html
ChainSCReg html
Summary-BASiCS_Chain-method html
as.data.frame-methods html
dim-BASiCS_Chain-method html
dimnames-BASiCS_Chain-method html
displayChainBASiCS-BASiCS_Chain-method
html
displaySummaryBASiCS-BASiCS_Summary-method
html
dot-generateSubsets html
format-methods html
makeExampleBASiCS_Data html
newBASiCS_Chain html
newBASiCS_Data html
plot-BASiCS_Chain-method html
plot-BASiCS_Summary-method html
rowData html
show-BASiCS_ResultDE-method html
show-BASiCS_ResultVG-method html
show-BASiCS_ResultsDE-method html
subset-BASiCS_Chain-method html
subset-methods 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 (BASiCS)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'mitch' is missing or broken
done
BASiCS.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(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, 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")
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.425
Average acceptance rate among mu[i]'s: 0.7085
Maximum acceptance rate among mu[i]'s: 0.875
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.6505
Maximum acceptance rate among delta[i]'s: 0.925
Minimum acceptance rate among nu[jk]'s: 0.875
Average acceptance rate among nu[jk]'s: 0.96
Maximum acceptance rate among nu[jk]'s: 1
Minimum acceptance rate among theta[k]'s: 0.875
Average acceptance rate among theta[k]'s: 0.875
Maximum acceptance rate among theta[k]'s: 0.875
-----------------------------------------------------
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 427 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 427 ]
>
> proc.time()
user system elapsed
152.48 1.48 154.17
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 2.57 | 0.15 | 2.73 | |
| BASiCS_Chain | 3.32 | 0.05 | 3.38 | |
| BASiCS_CorrectOffset | 0.02 | 0.00 | 0.02 | |
| BASiCS_DenoisedCounts | 2.44 | 0.03 | 2.47 | |
| BASiCS_DenoisedRates | 2.14 | 0.03 | 2.17 | |
| BASiCS_DetectVG | 0.45 | 0.06 | 0.51 | |
| BASiCS_DiagHist | 0.92 | 0.00 | 0.92 | |
| BASiCS_DiagPlot | 0.47 | 0.00 | 0.47 | |
| BASiCS_DivideAndConquer | 1.86 | 0.02 | 15.03 | |
| BASiCS_Draw | 0.5 | 0.0 | 0.5 | |
| BASiCS_EffectiveSize | 0.17 | 0.00 | 0.18 | |
| BASiCS_Filter | 0 | 0 | 0 | |
| BASiCS_LoadChain | 1.83 | 0.00 | 1.82 | |
| BASiCS_MCMC | 5.66 | 0.03 | 5.69 | |
| BASiCS_MockSCE | 0.42 | 0.00 | 0.42 | |
| BASiCS_PlotDE | 3.64 | 0.03 | 3.67 | |
| BASiCS_PlotOffset | 0.68 | 0.00 | 0.67 | |
| BASiCS_PlotVG | 0.28 | 0.02 | 0.30 | |
| BASiCS_PriorParam | 0.26 | 0.00 | 0.27 | |
| BASiCS_ShowFit | 0.19 | 0.01 | 0.20 | |
| BASiCS_Sim | 0.64 | 0.00 | 0.64 | |
| BASiCS_Summary-methods | 0 | 0 | 0 | |
| BASiCS_Summary | 2.28 | 0.00 | 2.28 | |
| BASiCS_TestDE | 6.72 | 0.03 | 6.75 | |
| BASiCS_VarThresholdSearchHVG_LVG | 1.83 | 0.04 | 1.86 | |
| BASiCS_VarianceDecomp | 0.14 | 0.01 | 0.15 | |
| Summary-BASiCS_Chain-method | 0.06 | 0.00 | 0.07 | |
| dim-BASiCS_Chain-method | 0.00 | 0.02 | 0.01 | |
| dimnames-BASiCS_Chain-method | 0 | 0 | 0 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.16 | 0.03 | 0.24 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.13 | 0.01 | 0.16 | |
| makeExampleBASiCS_Data | 0.36 | 0.00 | 0.36 | |
| newBASiCS_Chain | 4.30 | 0.04 | 4.33 | |
| plot-BASiCS_Chain-method | 0.2 | 0.0 | 0.2 | |
| plot-BASiCS_Summary-method | 0.14 | 0.07 | 0.24 | |
| show-BASiCS_ResultDE-method | 0.11 | 0.03 | 0.15 | |
| show-BASiCS_ResultVG-method | 0.14 | 0.02 | 0.18 | |
| show-BASiCS_ResultsDE-method | 0.10 | 0.09 | 0.20 | |
| subset-BASiCS_Chain-method | 0.98 | 0.02 | 1.00 | |