Package: BASiCS

Version: 1.0.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BASiCS_1.0.1.tar.gz

StartedAt: 2018-04-11 21:39:13 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:43:00 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 226.5 seconds

RetCode: 0

Status:  OK

CheckDir: BASiCS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BASiCS_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘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 ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.0Mb
* 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 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_DenoisedRates  6.972  0.004   6.995
BASiCS_DenoisedCounts 6.644  0.092   6.739
BASiCS_MCMC           5.556  0.140   5.712
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

* 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)

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 

name	user	system	elapsed
BASiCS_Chain-methods	1.208	0.004	1.223
BASiCS_Chain	1.268	0.012	1.281
BASiCS_D_TestDE	0.168	0.028	1.547
BASiCS_DenoisedCounts	6.644	0.092	6.739
BASiCS_DenoisedRates	6.972	0.004	6.995
BASiCS_DetectHVG_LVG	0.116	0.024	0.150
BASiCS_Filter	0.052	0.008	0.060
BASiCS_LoadChain	0.460	0.064	0.523
BASiCS_MCMC	5.556	0.140	5.712
BASiCS_Sim	0.040	0.000	0.043
BASiCS_Summary-methods	0.096	0.032	0.130
BASiCS_Summary	0.692	0.084	0.780
BASiCS_TestDE	1.464	0.020	1.485
BASiCS_VarThresholdSearchHVG_LVG	0.108	0.016	0.130
BASiCS_VarianceDecomp	0.116	0.024	0.151
Summary-BASiCS_Chain-method	0.144	0.028	0.178
displayChainBASiCS-BASiCS_Chain-method	0.104	0.028	0.138
displaySummaryBASiCS-BASiCS_Summary-method	0.100	0.024	0.130
makeExampleBASiCS_Data	0.032	0.008	0.045
newBASiCS_Chain	0.464	0.052	0.518
newBASiCS_Data	0.092	0.004	0.097
plot-BASiCS_Chain-method	0.100	0.016	0.125
plot-BASiCS_Summary-method	0.108	0.020	0.133