Alan O'Callaghan
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/BASiCS |
| git_branch: RELEASE_3_13 |
| git_last_commit: 385fa3d |
| git_last_commit_date: 2021-05-19 12:30:39 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:35 -0400 (Fri, 15 Oct 2021).
|
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 121/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.4.0 (landing page) Alan O'Callaghan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BASiCS |
| Version: 2.4.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BASiCS_2.4.0.tar.gz |
| StartedAt: 2021-10-14 08:56:30 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:05:33 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 542.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BASiCS_2.4.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘2.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BASiCS’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 5.0Mb
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BASiCS_MCMC 8.823 0.031 8.865
BASiCS_Chain 5.977 0.708 6.685
newBASiCS_Chain 6.285 0.036 6.322
BASiCS_TestDE 5.842 0.012 5.855
BASiCS_DivideAndConquer 2.837 0.025 15.469
* 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
‘/home/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c BASiCS.cpp -o BASiCS.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 402 ]
>
> proc.time()
user system elapsed
278.152 3.061 281.332
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 4.121 | 0.460 | 4.582 | |
| BASiCS_Chain | 5.977 | 0.708 | 6.685 | |
| BASiCS_CorrectOffset | 0.012 | 0.008 | 0.020 | |
| BASiCS_DenoisedCounts | 3.565 | 0.028 | 3.593 | |
| BASiCS_DenoisedRates | 3.258 | 0.000 | 3.258 | |
| BASiCS_DetectVG | 0.559 | 0.004 | 0.563 | |
| BASiCS_DiagHist | 0.935 | 0.003 | 0.939 | |
| BASiCS_DiagPlot | 0.524 | 0.000 | 0.523 | |
| BASiCS_DivideAndConquer | 2.837 | 0.025 | 15.469 | |
| BASiCS_Draw | 0.756 | 0.000 | 0.756 | |
| BASiCS_EffectiveSize | 0.209 | 0.000 | 0.208 | |
| BASiCS_Filter | 0.003 | 0.000 | 0.003 | |
| BASiCS_LoadChain | 3.136 | 0.012 | 3.153 | |
| BASiCS_MCMC | 8.823 | 0.031 | 8.865 | |
| BASiCS_MockSCE | 0.597 | 0.000 | 0.596 | |
| BASiCS_PlotDE | 2.864 | 0.028 | 2.891 | |
| BASiCS_PlotOffset | 0.71 | 0.00 | 0.71 | |
| BASiCS_PlotVG | 0.315 | 0.008 | 0.324 | |
| BASiCS_PriorParam | 0.512 | 0.000 | 0.512 | |
| BASiCS_ShowFit | 0.185 | 0.004 | 0.189 | |
| BASiCS_Sim | 1.307 | 0.008 | 1.315 | |
| BASiCS_Summary-methods | 0.005 | 0.000 | 0.004 | |
| BASiCS_Summary | 3.256 | 0.008 | 3.264 | |
| BASiCS_TestDE | 5.842 | 0.012 | 5.855 | |
| BASiCS_VarThresholdSearchHVG_LVG | 1.740 | 0.008 | 1.747 | |
| BASiCS_VarianceDecomp | 0.183 | 0.004 | 0.187 | |
| Summary-BASiCS_Chain-method | 0.041 | 0.004 | 0.045 | |
| dim-BASiCS_Chain-method | 0.005 | 0.004 | 0.008 | |
| dimnames-BASiCS_Chain-method | 0.004 | 0.004 | 0.009 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.138 | 0.020 | 0.166 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.099 | 0.025 | 0.124 | |
| makeExampleBASiCS_Data | 0.577 | 0.000 | 0.578 | |
| newBASiCS_Chain | 6.285 | 0.036 | 6.322 | |
| plot-BASiCS_Chain-method | 0.095 | 0.012 | 0.107 | |
| plot-BASiCS_Summary-method | 0.097 | 0.007 | 0.105 | |
| show-BASiCS_ResultDE-method | 0.094 | 0.014 | 0.108 | |
| show-BASiCS_ResultVG-method | 0.088 | 0.016 | 0.103 | |
| show-BASiCS_ResultsDE-method | 0.096 | 0.006 | 0.102 | |
| subset-BASiCS_Chain-method | 0.817 | 0.008 | 0.825 | |