Back to Multiple platform build/check report for BioC 3.9
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BPRMeth on malbec2

This page was generated on 2019-04-09 11:47:06 -0400 (Tue, 09 Apr 2019).

Package 178/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.9.4
Chantriolnt-Andreas Kapourani
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BPRMeth
Branch: master
Last Commit: abc23bd
Last Changed Date: 2019-02-16 06:30:29 -0400 (Sat, 16 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: BPRMeth
Version: 1.9.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz
StartedAt: 2019-04-08 23:06:57 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:09:32 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 155.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BPRMeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BPRMeth’ version ‘1.9.4’
* 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 ‘BPRMeth’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    libs      1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bpr_cluster_wrap        5.911  0.023   5.936
cluster_profiles_mle    5.840  0.003   5.852
old_boxplot_cluster_gex 5.576  0.000   5.576
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.



Installation output

BPRMeth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BPRMeth
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BPRMeth’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c model_likelihood.cpp -o model_likelihood.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-BPRMeth/00new/BPRMeth/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 (BPRMeth)

Tests output

BPRMeth.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(BPRMeth)
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, colMeans, colSums, 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, 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
> 
> test_check("BPRMeth")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 70 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.934   0.179   5.100 

Example timings

BPRMeth.Rcheck/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr3.8090.0283.215
bpr_cluster_wrap5.9110.0235.936
bpr_optimize2.0630.0002.063
bpr_predict_wrap1.5470.0041.551
cluster_profiles_mle5.8400.0035.852
cluster_profiles_vb4.4120.0004.412
create_anno_region0.4610.0010.157
create_basis0.0020.0000.002
create_region_object0.0010.0000.000
design_matrix0.0040.0000.004
eval_functions0.0050.0000.004
infer_profiles_gibbs3.2140.0003.215
infer_profiles_mle1.6210.0001.621
infer_profiles_vb2.3090.0082.317
inner_predict_model_expr0.0070.0000.007
inner_train_model_expr0.0210.0000.021
old_boxplot_cluster_gex5.5760.0005.576
old_plot_cluster_prof3.8320.0003.832
old_plot_fitted_profiles0.9240.0000.924
plot_cluster_profiles3.3460.0483.395
plot_infer_profiles1.8340.0001.835
plot_predicted_expr2.4030.0002.346
pool_bs_seq_rep0.7900.0110.588
predict_expr2.4600.0041.981
preprocess_bs_seq0.4180.0040.201
preprocess_final_HTS_data0.8400.0030.476
process_haib_caltech_wrap0.8630.0040.500
read_anno0.3460.0000.089
read_bs_encode_haib0.3200.0040.109
read_chrom_size0.1650.0000.030
read_expr0.0020.0000.007
read_met0.2350.0000.064
read_rna_encode_caltech0.4090.0000.187