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This page was generated on 2022-01-15 11:07:09 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BPRMeth on riesling1


To the developers/maintainers of the BPRMeth package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BPRMeth.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 206/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.21.1  (landing page)
Chantriolnt-Andreas Kapourani
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/BPRMeth
git_branch: master
git_last_commit: 1107237
git_last_commit_date: 2021-11-20 23:13:48 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BPRMeth
Version: 1.21.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BPRMeth.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BPRMeth_1.21.1.tar.gz
StartedAt: 2022-01-14 18:27:35 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 18:30:02 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 146.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BPRMeth.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BPRMeth_1.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BPRMeth.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BPRMeth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BPRMeth' version '1.21.1'
* 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 whether package 'BPRMeth' 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 ... 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 LazyData ... 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/BPRMeth/libs/x64/BPRMeth.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
cluster_profiles_mle  5.6   0.11     5.7
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/BPRMeth.Rcheck/00check.log'
for details.



Installation output

BPRMeth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BPRMeth
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BPRMeth' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c model_likelihood.cpp -o model_likelihood.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BPRMeth.dll tmp.def RcppExports.o model_likelihood.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BPRMeth/00new/BPRMeth/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BPRMeth'
    finding HTML links ... done
    BPRMeth                                 html  
    bernoulli_data                          html  
    beta_data                               html  
    binomial_data                           html  
    boxplot_cluster_expr                    html  
    bpr_cluster_wrap                        html  
    bpr_optimize                            html  
    bpr_predict_wrap                        html  
    cluster_profiles_mle                    html  
    cluster_profiles_vb                     html  
    create_anno_region                      html  
    create_basis                            html  
    create_region_object                    html  
    design_matrix                           html  
    encode_expr                             html  
    encode_met                              html  
    eval_functions                          html  
    gaussian_data                           html  
    gex_data                                html  
    impute_bulk_met                         html  
    infer_profiles_gibbs                    html  
    infer_profiles_mle                      html  
    infer_profiles_vb                       html  
    inner_predict_model_expr                html  
    inner_train_model_expr                  html  
    meth_data                               html  
    model_log_likelihood                    html  
    old_boxplot_cluster_gex                 html  
    old_plot_cluster_prof                   html  
    old_plot_fitted_profiles                html  
    partition_bulk_dataset                  html  
    plot_cluster_profiles                   html  
    plot_infer_profiles                     html  
    finding level-2 HTML links ... done

    plot_predicted_expr                     html  
    pool_bs_seq_rep                         html  
    predict_expr                            html  
    preprocess_bs_seq                       html  
    preprocess_final_HTS_data               html  
    process_haib_caltech_wrap               html  
    read_anno                               html  
    read_bs_encode_haib                     html  
    read_chrom_size                         html  
    read_expr                               html  
    read_met                                html  
    read_rna_encode_caltech                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BPRMeth)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'wiggleplotr' is missing or broken
 done

Tests output

BPRMeth.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("BPRMeth")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ]
> 
> proc.time()
   user  system elapsed 
   3.06    0.42    3.45 

Example timings

BPRMeth.Rcheck/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr3.390.363.75
bpr_cluster_wrap3.920.013.95
bpr_optimize0.960.000.97
bpr_predict_wrap0.720.000.72
cluster_profiles_mle5.600.115.70
cluster_profiles_vb3.670.113.78
create_anno_region0.050.020.06
create_basis000
create_region_object000
design_matrix000
eval_functions000
impute_bulk_met0.50.00.5
infer_profiles_gibbs1.750.001.75
infer_profiles_mle1.120.001.13
infer_profiles_vb2.160.002.15
inner_predict_model_expr0.010.000.02
inner_train_model_expr0.020.000.02
old_boxplot_cluster_gex3.590.003.59
old_plot_cluster_prof3.740.003.73
old_plot_fitted_profiles0.670.000.68
partition_bulk_dataset0.030.000.03
plot_cluster_profiles3.550.183.73
plot_infer_profiles2.230.022.28
plot_predicted_expr1.950.021.97
pool_bs_seq_rep0.190.010.20
predict_expr1.530.021.55
preprocess_bs_seq0.080.000.08
preprocess_final_HTS_data0.20.00.2
process_haib_caltech_wrap0.240.000.24
read_anno0.010.000.01
read_bs_encode_haib0.050.000.05
read_chrom_size000
read_expr000
read_met0.020.000.01
read_rna_encode_caltech0.070.000.08