CHECK report for BASiCS on malbec1
This page was generated on 2018-04-12 13:16:46 -0400 (Thu, 12 Apr 2018).
BASiCS 1.0.1 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) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Command output
Installation output
BASiCS.Rcheck/00install.out
* installing *source* package ‘BASiCS’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
BASiCS_CPPcode.cpp: In function ‘arma::mat muUpdateNoSpikes(const vec&, const vec&, const double&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, const int&, const uvec&, const uvec&, const int&)’:
BASiCS_CPPcode.cpp:1226:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < ConstrainGene.size(); i++)
^
BASiCS_CPPcode.cpp:1251:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < NotConstrainGene.size(); i++)
^
BASiCS_CPPcode.cpp: In function ‘Rcpp::List HiddenBASiCS_MCMCcppNoSpikes(int, int, int, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, double, double, double, double, double, double, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)’:
BASiCS_CPPcode.cpp:1648:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(i%Thin==0 & i>=Burn)
^
BASiCS_CPPcode.cpp:1666:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(i%(2*Thin) == 0 & PrintProgress == 1)
^
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS_CPPcode.o RcppExports.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/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)
Tests output
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-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, 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
12.012 0.196 12.212
Example timings
BASiCS.Rcheck/BASiCS-Ex.timings