Catalina Vallejos
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BASiCS |
| Branch: RELEASE_3_11 |
| Last Commit: 15fd420 |
| Last Changed Date: 2020-04-27 15:10:45 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:24 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BASiCS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 115/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BASiCS 2.0.0 Catalina Vallejos
| malbec2 | Linux (Ubuntu 18.04.4 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: 2.0.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BASiCS_2.0.0.tar.gz |
| StartedAt: 2020-10-16 23:04:31 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:11:00 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 388.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BASiCS_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BASiCS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.0.0’
* 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 15.3Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 12.4Mb
* 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 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_TestDE 9.238 0 9.239
* 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-3.11-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c general_utils.cpp -o general_utils.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
>
> test_check("BASiCS")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 356 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
112.268 0.649 112.946
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 1.217 | 0.016 | 2.101 | |
| BASiCS_Chain | 2.331 | 0.011 | 2.344 | |
| BASiCS_CorrectOffset | 0.023 | 0.000 | 0.023 | |
| BASiCS_DenoisedCounts | 1.855 | 0.003 | 1.859 | |
| BASiCS_DenoisedRates | 1.342 | 0.001 | 1.341 | |
| BASiCS_DetectVG | 0.881 | 0.047 | 0.930 | |
| BASiCS_DiagHist | 1.101 | 0.012 | 1.113 | |
| BASiCS_DiagPlot | 0.664 | 0.004 | 0.668 | |
| BASiCS_Draw | 0.365 | 0.000 | 0.365 | |
| BASiCS_EffectiveSize | 0.255 | 0.000 | 0.255 | |
| BASiCS_Filter | 0.145 | 0.000 | 0.145 | |
| BASiCS_LoadChain | 0.926 | 0.004 | 0.930 | |
| BASiCS_MCMC | 4.107 | 0.004 | 4.111 | |
| BASiCS_PlotDE | 4.694 | 0.008 | 4.804 | |
| BASiCS_PlotOffset | 1.131 | 0.004 | 1.136 | |
| BASiCS_PlotVG | 0.418 | 0.004 | 0.422 | |
| BASiCS_PriorParam | 0.185 | 0.004 | 0.188 | |
| BASiCS_ShowFit | 0.245 | 0.004 | 0.248 | |
| BASiCS_Sim | 0.417 | 0.000 | 0.417 | |
| BASiCS_Summary-methods | 0.004 | 0.000 | 0.005 | |
| BASiCS_Summary | 1.181 | 0.000 | 1.180 | |
| BASiCS_TestDE | 9.238 | 0.000 | 9.239 | |
| BASiCS_VarThresholdSearchHVG_LVG | 4.580 | 0.008 | 4.588 | |
| BASiCS_VarianceDecomp | 0.202 | 0.004 | 0.205 | |
| Summary-BASiCS_Chain-method | 0.055 | 0.000 | 0.054 | |
| dim-BASiCS_Chain-method | 0.007 | 0.000 | 0.006 | |
| dimnames-BASiCS_Chain-method | 0.007 | 0.000 | 0.007 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.149 | 0.069 | 1.347 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.164 | 0.081 | 0.247 | |
| makeExampleBASiCS_Data | 0.272 | 0.024 | 0.296 | |
| newBASiCS_Chain | 2.342 | 0.128 | 2.470 | |
| newBASiCS_Data | 0.392 | 0.000 | 0.393 | |
| plot-BASiCS_Chain-method | 0.099 | 0.047 | 0.147 | |
| plot-BASiCS_Summary-method | 0.194 | 0.071 | 0.266 | |
| show-BASiCS_ResultDE-method | 0.151 | 0.082 | 0.233 | |
| show-BASiCS_ResultVG-method | 0.112 | 0.060 | 0.171 | |
| show-BASiCS_ResultsDE-method | 0.143 | 0.076 | 0.219 | |
| subset-BASiCS_Chain-method | 0.108 | 0.008 | 0.116 | |