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CHECK report for RJMCMCNucleosomes on malbec1

This page was generated on 2021-05-06 12:28:51 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RJMCMCNucleosomes package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1537/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 1.14.0  (landing page)
Astrid Deschênes
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RJMCMCNucleosomes
Branch: RELEASE_3_12
Last Commit: 1638992
Last Changed Date: 2020-10-27 11:20:36 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RJMCMCNucleosomes
Version: 1.14.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RJMCMCNucleosomes_1.14.0.tar.gz
StartedAt: 2021-05-06 05:18:41 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:22:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 232.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RJMCMCNucleosomes_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RJMCMCNucleosomes’ 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.12-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’
for details.



Installation output

RJMCMCNucleosomes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RJMCMCNucleosomes
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘RJMCMCNucleosomes’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c NucleoDirichlet.cpp -o NucleoDirichlet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Nucleosome.cpp -o Nucleosome.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c SegmentSeq.cpp -o SegmentSeq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-RJMCMCNucleosomes/00new/RJMCMCNucleosomes/libs
** R
** data
** 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 (RJMCMCNucleosomes)

Tests output

RJMCMCNucleosomes.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("RJMCMCNucleosomes")

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, 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


Attaching package: 'S4Vectors'

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

    expand.grid

RJMCMCNucleosomes - Predicted nucleosomes

Call:
rjmcmc(reads = reads_demo_02, seqName = "chr_SYNTHETIC", nbrIterations = 1e+05, 
    kMax = 30, lambda = 2, minInterval = 146, maxInterval = 490, 
    minReads = 3, vSeed = 32)

Number of nucleosomes:
[1] 6

Nucleosomes positions:
GRanges object with 6 ranges and 0 metadata columns:
           seqnames    ranges strand
              <Rle> <IRanges>  <Rle>
  [1] chr_SYNTHETIC     10072      *
  [2] chr_SYNTHETIC     10241      *
  [3] chr_SYNTHETIC     10574      *
  [4] chr_SYNTHETIC     10656      *
  [5] chr_SYNTHETIC     10669      *
  [6] chr_SYNTHETIC     10744      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: out/results/rjmcmc_seg_1.rds"
[1] "Done: out/results/rjmcmc_seg_1.rds"
[1] "Doing: out/results/rjmcmc_seg_2.rds"
[1] "Done: out/results/rjmcmc_seg_2.rds"
[1] "Doing: out/results/rjmcmc_seg_3.rds"
[1] "Done: out/results/rjmcmc_seg_3.rds"
[1] "Doing: out/results/rjmcmc_seg_4.rds"
[1] "Done: out/results/rjmcmc_seg_4.rds"
[1] "Doing: out/results/rjmcmc_seg_5.rds"
[1] "Done: out/results/rjmcmc_seg_5.rds"
[1] "Doing: out/results/rjmcmc_seg_6.rds"
[1] "Done: out/results/rjmcmc_seg_6.rds"
[1] "Doing: out/results/rjmcmc_seg_7.rds"
[1] "Done: out/results/rjmcmc_seg_7.rds"
[1] "Doing: out/results/rjmcmc_seg_8.rds"
[1] "Done: out/results/rjmcmc_seg_8.rds"
[1] "Doing: out/results/rjmcmc_seg_9.rds"
[1] "Done: out/results/rjmcmc_seg_9.rds"
[1] "Doing: out/results/rjmcmc_seg_10.rds"
[1] "Done: out/results/rjmcmc_seg_10.rds"
[1] "Doing: out/results/rjmcmc_seg_11.rds"
[1] "Done: out/results/rjmcmc_seg_11.rds"
[1] "Doing: out/results/rjmcmc_seg_12.rds"
[1] "Done: out/results/rjmcmc_seg_12.rds"
[1] "Doing: out/results/rjmcmc_seg_13.rds"
[1] "Done: out/results/rjmcmc_seg_13.rds"
[1] "Doing: out/results/rjmcmc_seg_14.rds"
[1] "Done: out/results/rjmcmc_seg_14.rds"
[1] "Doing: out/results/rjmcmc_seg_15.rds"
[1] "Done: out/results/rjmcmc_seg_15.rds"
[1] "Doing: out/results/rjmcmc_seg_16.rds"
[1] "Done: out/results/rjmcmc_seg_16.rds"
[1] "Doing: out/results/rjmcmc_seg_17.rds"
[1] "Done: out/results/rjmcmc_seg_17.rds"
[1] "Doing: out/results/rjmcmc_seg_18.rds"
[1] "Done: out/results/rjmcmc_seg_18.rds"
[1] "Doing: out/results/rjmcmc_seg_19.rds"
[1] "Done: out/results/rjmcmc_seg_19.rds"
[1] "Doing: out/results/rjmcmc_seg_20.rds"
[1] "Done: out/results/rjmcmc_seg_20.rds"
[1] "Doing: out/results/rjmcmc_seg_21.rds"
[1] "Done: out/results/rjmcmc_seg_21.rds"
[1] "Doing: out/results/rjmcmc_seg_22.rds"
[1] "Done: out/results/rjmcmc_seg_22.rds"
[1] "Doing: out/results/rjmcmc_seg_23.rds"
[1] "Done: out/results/rjmcmc_seg_23.rds"
[1] "Doing: out/results/rjmcmc_seg_24.rds"
[1] "Done: out/results/rjmcmc_seg_24.rds"
[1] "Doing: out/results/rjmcmc_seg_25.rds"
[1] "Done: out/results/rjmcmc_seg_25.rds"
[1] "Doing: out/results/rjmcmc_seg_26.rds"
[1] "Done: out/results/rjmcmc_seg_26.rds"
[1] "Doing: out/results/rjmcmc_seg_27.rds"
[1] "Done: out/results/rjmcmc_seg_27.rds"
[1] "Doing: out/results/rjmcmc_seg_28.rds"
[1] "Done: out/results/rjmcmc_seg_28.rds"
[1] "Doing: out/results/rjmcmc_seg_29.rds"
[1] "Done: out/results/rjmcmc_seg_29.rds"
[1] "Doing: out/results/rjmcmc_seg_30.rds"
[1] "Done: out/results/rjmcmc_seg_30.rds"
[1] "Doing: out/results/rjmcmc_seg_31.rds"
[1] "Done: out/results/rjmcmc_seg_31.rds"
[1] "Doing: out/results/rjmcmc_seg_32.rds"
[1] "Done: out/results/rjmcmc_seg_32.rds"
[1] "Doing: out/results/rjmcmc_seg_33.rds"
[1] "Done: out/results/rjmcmc_seg_33.rds"
[1] "Doing: out/results/rjmcmc_seg_34.rds"
[1] "Done: out/results/rjmcmc_seg_34.rds"
[1] "Doing: out/results/rjmcmc_seg_35.rds"
[1] "Done: out/results/rjmcmc_seg_35.rds"
[1] "Doing: out/results/rjmcmc_seg_36.rds"
[1] "Done: out/results/rjmcmc_seg_36.rds"
[1] "Doing: out/results/rjmcmc_seg_37.rds"
[1] "Done: out/results/rjmcmc_seg_37.rds"
[1] "Doing: out/results/rjmcmc_seg_38.rds"
[1] "Done: out/results/rjmcmc_seg_38.rds"
[1] "Doing: out/results/rjmcmc_seg_39.rds"
[1] "Done: out/results/rjmcmc_seg_39.rds"
[1] "Doing: out/results/rjmcmc_seg_40.rds"
[1] "Done: out/results/rjmcmc_seg_40.rds"
[1] "Doing: out/results/rjmcmc_seg_41.rds"
[1] "Done: out/results/rjmcmc_seg_41.rds"
[1] "Doing: out/results/rjmcmc_seg_42.rds"
[1] "Done: out/results/rjmcmc_seg_42.rds"
[1] "Doing: out/results/rjmcmc_seg_43.rds"
[1] "Done: out/results/rjmcmc_seg_43.rds"
[1] "Doing: out/results/rjmcmc_seg_44.rds"
[1] "Done: out/results/rjmcmc_seg_44.rds"
[1] "Doing: out/results/rjmcmc_seg_45.rds"
[1] "Done: out/results/rjmcmc_seg_45.rds"
[1] "Doing: out/results/rjmcmc_seg_46.rds"
[1] "Done: out/results/rjmcmc_seg_46.rds"
[1] "Doing: out/results/rjmcmc_seg_47.rds"
[1] "Done: out/results/rjmcmc_seg_47.rds"
[1] "Doing: out/results/rjmcmc_seg_48.rds"
[1] "Done: out/results/rjmcmc_seg_48.rds"
[1] "Doing: out/results/rjmcmc_seg_49.rds"
[1] "Done: out/results/rjmcmc_seg_49.rds"
[1] "Doing: out/results/rjmcmc_seg_50.rds"
[1] "Done: out/results/rjmcmc_seg_50.rds"
[1] "Doing: out/results/rjmcmc_seg_51.rds"
[1] "Done: out/results/rjmcmc_seg_51.rds"
[1] "Doing: out/results/rjmcmc_seg_52.rds"
[1] "Done: out/results/rjmcmc_seg_52.rds"
[1] "Doing: out/results/rjmcmc_seg_53.rds"
[1] "Done: out/results/rjmcmc_seg_53.rds"
[1] "Doing: out/results/rjmcmc_seg_54.rds"
[1] "Done: out/results/rjmcmc_seg_54.rds"
[1] "Doing: out/results/rjmcmc_seg_55.rds"
[1] "Done: out/results/rjmcmc_seg_55.rds"
[1] "Doing: out/results/rjmcmc_seg_56.rds"
[1] "Done: out/results/rjmcmc_seg_56.rds"

RJMCMCNucleosomes - Predicted nucleosomes Before and After Post-Treatment
BEFORE POST-TREATMENT
Number of nucleosomes:
[1] 102

Nucleosomes positions:
GRanges object with 102 ranges and 0 metadata columns:
             seqnames    ranges strand
                <Rle> <IRanges>  <Rle>
    [1] chr_SYNTHETIC      1255      *
    [2] chr_SYNTHETIC      2259      *
    [3] chr_SYNTHETIC      3623      *
    [4] chr_SYNTHETIC      4259      *
    [5] chr_SYNTHETIC      5348      *
    ...           ...       ...    ...
   [98] chr_SYNTHETIC     53427      *
   [99] chr_SYNTHETIC     54220      *
  [100] chr_SYNTHETIC     54771      *
  [101] chr_SYNTHETIC     55358      *
  [102] chr_SYNTHETIC     55936      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

AFTER POST-TREATMENT
Number of nucleosomes:
[1] 89

Nucleosomes positions:
GRanges object with 89 ranges and 0 metadata columns:
            seqnames    ranges strand
               <Rle> <IRanges>  <Rle>
   [1] chr_SYNTHETIC      1255      *
   [2] chr_SYNTHETIC      2259      *
   [3] chr_SYNTHETIC      3623      *
   [4] chr_SYNTHETIC      4259      *
   [5] chr_SYNTHETIC      5348      *
   ...           ...       ...    ...
  [85] chr_SYNTHETIC     53286      *
  [86] chr_SYNTHETIC     54220      *
  [87] chr_SYNTHETIC     54771      *
  [88] chr_SYNTHETIC     55358      *
  [89] chr_SYNTHETIC     55936      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

RJMCMCNucleosomes - Predicted nucleosomes

Number of nucleosomes:
[1] 11

Nucleosomes positions:
GRanges object with 11 ranges and 0 metadata columns:
            seqnames    ranges strand
               <Rle> <IRanges>  <Rle>
   [1] chr_SYNTHETIC     10077      *
   [2] chr_SYNTHETIC     10236      *
   [3] chr_SYNTHETIC     10406      *
   [4] chr_SYNTHETIC     10571      *
   [5] chr_SYNTHETIC     10744      *
   [6] chr_SYNTHETIC     10842      *
   [7] chr_SYNTHETIC     10846      *
   [8] chr_SYNTHETIC     10896      *
   [9] chr_SYNTHETIC     10906      *
  [10] chr_SYNTHETIC     11410      *
  [11] chr_SYNTHETIC     11580      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Doing: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"


RUNIT TEST PROTOCOL -- Thu May  6 05:22:30 2021 
*********************************************** 
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RJMCMCNucleosomes RUnit Tests - 86 test functions, 0 errors, 0 failures
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 24.772   0.516  36.902 

Example timings

RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result0.6000.0440.643
mergeAllRDSFiles0.2840.0000.298
mergeAllRDSFilesFromDirectory0.20.00.2
mergeRDSFiles0.1880.0200.211
plotNucleosomes0.6120.0200.634
postMerge0.9840.0080.991
postTreatment0.480.000.48
print.rjmcmcNucleosomes0.0080.0000.009
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.0800.0040.082
print.rjmcmcNucleosomesMerge0.1320.0040.134
reads_demo_010.0360.0000.035
reads_demo_020.0440.0000.046
rjmcmc0.1040.0040.106
rjmcmcCHR0.0440.0040.049
rjmcmcNucleo0.0760.0040.081
runCHR0.0680.0000.069
segmentation0.0880.0080.095
validateDirectoryParameters0.0000.0000.001
validatePlotNucleosomesParameters0.0000.0040.003
validatePrepMergeParameters0.0040.0000.002
validateRDSFilesParameters0.0000.0000.001
validateRJMCMCParameters0.0120.0000.009
validateSegmentationParameters0.0160.0000.016