Catalina A. Vallejos
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/BASiCS |
| Branch: RELEASE_3_6 |
| Last Commit: dba7914 |
| Last Changed Date: 2018-03-18 15:01:01 -0400 (Sun, 18 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:45:47 -0400 (Thu, 12 Apr 2018).
| Package 93/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BASiCS 1.0.1 Catalina A. Vallejos
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BASiCS |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BASiCS_1.0.1.tar.gz |
| StartedAt: 2018-04-12 00:42:36 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:47:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 294.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BASiCS_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.1’
* 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BASiCS_MCMC 7.489 0.251 7.974
* 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: OK
BASiCS.Rcheck/00install.out
* installing *source* package ‘BASiCS’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
In file included from BASiCS_CPPcode.cpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:138:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:106:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -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_CPPcode.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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck/BASiCS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BASiCS)
BASiCS.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 object is masked from 'package:base':
apply
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: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.462
Average acceptance rate among mu[i]'s: 0.69876
Maximum acceptance rate among mu[i]'s: 0.856
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.58256
Maximum acceptance rate among delta[i]'s: 0.682
Acceptance rate for phi (joint): 0.896
Minimum acceptance rate among nu[j]'s: 0.468
Average acceptance rate among nu[j]'s: 0.5527
Maximum acceptance rate among nu[j]'s: 0.714
Minimum acceptance rate among theta[k]'s: 0.78
Average acceptance rate among theta[k]'s: 0.78
Maximum acceptance rate among theta[k]'s: 0.78
-------------------------------------------------------------
-------------------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.514
Average acceptance rate among mu[i]'s: 0.70912
Maximum acceptance rate among mu[i]'s: 0.832
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.5884
Maximum acceptance rate among delta[i]'s: 0.736
Acceptance rate for phi (joint): 0.898
Minimum acceptance rate among nu[j]'s: 0.42
Average acceptance rate among nu[j]'s: 0.5339
Maximum acceptance rate among nu[j]'s: 0.762
Minimum acceptance rate among theta[k]'s: 0.828
Average acceptance rate among theta[k]'s: 0.835
Maximum acceptance rate among theta[k]'s: 0.842
-------------------------------------------------------------
══ testthat results ═══════════════════════════════════════════════════════════
OK: 39 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.304 0.438 16.252
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 1.291 | 0.009 | 1.322 | |
| BASiCS_Chain | 1.673 | 0.042 | 1.792 | |
| BASiCS_D_TestDE | 0.168 | 0.026 | 0.223 | |
| BASiCS_DenoisedCounts | 4.757 | 0.047 | 4.933 | |
| BASiCS_DenoisedRates | 4.781 | 0.014 | 4.965 | |
| BASiCS_DetectHVG_LVG | 0.147 | 0.017 | 0.171 | |
| BASiCS_Filter | 0.052 | 0.001 | 0.055 | |
| BASiCS_LoadChain | 0.434 | 0.003 | 0.455 | |
| BASiCS_MCMC | 7.489 | 0.251 | 7.974 | |
| BASiCS_Sim | 0.054 | 0.000 | 0.056 | |
| BASiCS_Summary-methods | 0.149 | 0.016 | 0.171 | |
| BASiCS_Summary | 0.521 | 0.009 | 0.551 | |
| BASiCS_TestDE | 2.019 | 0.070 | 2.180 | |
| BASiCS_VarThresholdSearchHVG_LVG | 0.153 | 0.017 | 0.177 | |
| BASiCS_VarianceDecomp | 0.153 | 0.017 | 0.176 | |
| Summary-BASiCS_Chain-method | 0.150 | 0.016 | 0.173 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.153 | 0.015 | 0.178 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.146 | 0.016 | 0.172 | |
| makeExampleBASiCS_Data | 0.047 | 0.000 | 0.048 | |
| newBASiCS_Chain | 0.460 | 0.004 | 0.475 | |
| newBASiCS_Data | 0.098 | 0.001 | 0.101 | |
| plot-BASiCS_Chain-method | 0.151 | 0.016 | 0.170 | |
| plot-BASiCS_Summary-method | 0.150 | 0.015 | 0.169 | |