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 11:05:59 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.10.5.tar.gz |
| StartedAt: 2023-04-10 18:54:03 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:00:57 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 414.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/BASiCS.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 for sufficient/correct file permissions ... 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 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 6.450 0.102 6.580
BASiCS_TestDE 6.053 0.082 6.149
BASiCS_DivideAndConquer 2.289 0.061 23.733
* 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
‘/Users/biocbuild/bbs-3.16-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS.cpp -o BASiCS.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13) ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13) installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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
253.594 5.666 153.686
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 2.454 | 0.076 | 2.532 | |
| BASiCS_Chain | 3.767 | 0.076 | 3.848 | |
| BASiCS_CorrectOffset | 0.014 | 0.005 | 0.019 | |
| BASiCS_DenoisedCounts | 2.357 | 0.026 | 2.387 | |
| BASiCS_DenoisedRates | 2.235 | 0.017 | 2.256 | |
| BASiCS_DetectVG | 0.648 | 0.053 | 0.703 | |
| BASiCS_DiagHist | 0.829 | 0.020 | 0.850 | |
| BASiCS_DiagPlot | 0.553 | 0.011 | 0.565 | |
| BASiCS_DivideAndConquer | 2.289 | 0.061 | 23.733 | |
| BASiCS_Draw | 0.375 | 0.009 | 0.385 | |
| BASiCS_EffectiveSize | 0.180 | 0.010 | 0.189 | |
| BASiCS_Filter | 0.002 | 0.000 | 0.002 | |
| BASiCS_LoadChain | 1.850 | 0.022 | 1.874 | |
| BASiCS_MCMC | 6.450 | 0.102 | 6.580 | |
| BASiCS_MockSCE | 0.340 | 0.003 | 0.344 | |
| BASiCS_PlotDE | 2.814 | 0.035 | 2.857 | |
| BASiCS_PlotOffset | 0.939 | 0.012 | 0.954 | |
| BASiCS_PlotVG | 0.342 | 0.007 | 0.350 | |
| BASiCS_PriorParam | 0.340 | 0.006 | 0.348 | |
| BASiCS_ShowFit | 0.231 | 0.006 | 0.240 | |
| BASiCS_Sim | 0.737 | 0.006 | 0.744 | |
| BASiCS_Summary-methods | 0.004 | 0.002 | 0.005 | |
| BASiCS_Summary | 2.014 | 0.017 | 2.036 | |
| BASiCS_TestDE | 6.053 | 0.082 | 6.149 | |
| BASiCS_VarThresholdSearchHVG_LVG | 1.702 | 0.117 | 1.834 | |
| BASiCS_VarianceDecomp | 0.229 | 0.005 | 0.234 | |
| Summary-BASiCS_Chain-method | 0.064 | 0.008 | 0.074 | |
| dim-BASiCS_Chain-method | 0.005 | 0.003 | 0.009 | |
| dimnames-BASiCS_Chain-method | 0.005 | 0.003 | 0.007 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.116 | 0.050 | 0.226 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.114 | 0.033 | 0.166 | |
| makeExampleBASiCS_Data | 0.246 | 0.001 | 0.248 | |
| newBASiCS_Chain | 4.158 | 0.041 | 4.215 | |
| plot-BASiCS_Chain-method | 0.115 | 0.043 | 0.177 | |
| plot-BASiCS_Summary-method | 0.116 | 0.034 | 0.166 | |
| show-BASiCS_ResultDE-method | 0.101 | 0.034 | 0.148 | |
| show-BASiCS_ResultVG-method | 0.103 | 0.032 | 0.152 | |
| show-BASiCS_ResultsDE-method | 0.106 | 0.034 | 0.156 | |
| subset-BASiCS_Chain-method | 0.831 | 0.011 | 0.842 | |