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CHECK report for DEScan2 on tokay2

This page was generated on 2019-10-16 12:40:47 -0400 (Wed, 16 Oct 2019).

Package 422/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEScan2 1.4.0
Dario Righelli
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DEScan2
Branch: RELEASE_3_9
Last Commit: a5f2d38
Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 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 [ WARNINGS ] 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

Summary

Package: DEScan2
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEScan2_1.4.0.tar.gz
StartedAt: 2019-10-16 03:11:41 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:23:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 719.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DEScan2.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEScan2_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEScan2.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEScan2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEScan2' version '1.4.0'
* 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 'DEScan2' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeKXvfw/R.INSTALL23285d557249/DEScan2/man/finalRegions.Rd:34: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeKXvfw/R.INSTALL23285d557249/DEScan2/man/findPeaks.Rd:61: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEScan2.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DEScan2/libs/i386/DEScan2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DEScan2/libs/x64/DEScan2.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
findPeaks               28.58   2.50   31.78
binnedCoverage          14.22   1.39   16.80
finalRegions            14.89   0.11   15.08
findOverlapsOverSamples  9.67   0.00    9.67
countFinalRegions        4.20   1.64   13.86
readFilesAsGRangesList   3.50   1.03   11.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
findPeaks               22.15   2.58   25.58
finalRegions            23.23   0.03   23.33
binnedCoverage          17.11   2.31   20.33
findOverlapsOverSamples 10.72   0.00   10.72
countFinalRegions        4.50   1.01   13.14
readFilesAsGRangesList   3.51   0.66   10.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEScan2.Rcheck/00check.log'
for details.



Installation output

DEScan2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DEScan2_1.4.0.tar.gz && rm -rf DEScan2.buildbin-libdir && mkdir DEScan2.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEScan2.buildbin-libdir DEScan2_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DEScan2_1.4.0.zip && rm DEScan2_1.4.0.tar.gz DEScan2_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2471k  100 2471k    0     0  34.8M      0 --:--:-- --:--:-- --:--:-- 38.9M

install for i386

* installing *source* package 'DEScan2' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpparma_max_win.cpp -o rcpparma_max_win.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEScan2.buildbin-libdir/00LOCK-DEScan2/00new/DEScan2/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEScan2'
    finding HTML links ... done
    DEScan2                                 html  
    RleListToRleMatrix                      html  
    binToChrCoordMatRowNames                html  
    binnedCovOnly                           html  
    binnedCoverage                          html  
    c_get_disjoint_max_win                  html  
    computeCoverageMovingWindowOnChr        html  
    computeLambdaOnChr                      html  
    computeZ                                html  
    constructBedRanges                      html  
    countFinalRegions                       html  
    createGranges                           html  
    cutGRangesPerChromosome                 html  
    divideEachSampleByChromosomes           html  
    evenRunMean                             html  
    evenRunSum                              html  
    finalRegions                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeKXvfw/R.INSTALL23285d557249/DEScan2/man/finalRegions.Rd:34: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    findOverlapsOverSamples                 html  
    findPeaks                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeKXvfw/R.INSTALL23285d557249/DEScan2/man/findPeaks.Rd:61: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    fromSamplesToChrsGRangesList            html  
    generateDFofSamplesPerChromosomes       html  
    get_disjoint_max_win                    html  
    giveUniqueNamesToPeaksOverSamples       html  
    initMergedPeaksNames                    html  
    keepRelevantChrs                        html  
    rcpparma_get_disjoint_max_win           html  
    readBamAsBed                            html  
    readBedFile                             html  
    readFilesAsGRangesList                  html  
    saveGRangesAsBed                        html  
    saveGRangesAsTsv                        html  
    setGRGenomeInfo                         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

install for x64

* installing *source* package 'DEScan2' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpparma_max_win.cpp -o rcpparma_max_win.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEScan2.buildbin-libdir/DEScan2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEScan2' as DEScan2_1.4.0.zip
* DONE (DEScan2)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DEScan2' successfully unpacked and MD5 sums checked

Tests output

DEScan2.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("DEScan2")
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, 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, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb

> 
> test_check("DEScan2")
Maximizing with zthresh: 10	sigwin: 10
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  47.26    4.48   62.75 

DEScan2.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("DEScan2")
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, 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, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb

> 
> test_check("DEScan2")
Maximizing with zthresh: 10	sigwin: 10
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  38.96    3.12   51.17 

Example timings

DEScan2.Rcheck/examples_i386/DEScan2-Ex.timings

nameusersystemelapsed
RleListToRleMatrix0.150.000.16
binnedCoverage14.22 1.3916.80
constructBedRanges0.530.111.75
countFinalRegions 4.20 1.6413.86
createGranges0.170.061.13
cutGRangesPerChromosome0.050.000.04
divideEachSampleByChromosomes0.280.000.28
finalRegions14.89 0.1115.08
findOverlapsOverSamples9.670.009.67
findPeaks28.58 2.5031.78
fromSamplesToChrsGRangesList0.240.020.25
keepRelevantChrs0.030.000.04
readBamAsBed0.070.000.07
readBedFile0.110.000.13
readFilesAsGRangesList 3.50 1.0311.86
saveGRangesAsBed0.110.000.11
saveGRangesAsTsv0.020.000.01
setGRGenomeInfo0.200.061.03

DEScan2.Rcheck/examples_x64/DEScan2-Ex.timings

nameusersystemelapsed
RleListToRleMatrix0.180.000.19
binnedCoverage17.11 2.3120.33
constructBedRanges0.580.081.38
countFinalRegions 4.50 1.0113.14
createGranges0.170.130.94
cutGRangesPerChromosome0.060.000.06
divideEachSampleByChromosomes0.240.000.23
finalRegions23.23 0.0323.33
findOverlapsOverSamples10.72 0.0010.72
findPeaks22.15 2.5825.58
fromSamplesToChrsGRangesList0.30.00.3
keepRelevantChrs0.050.000.04
readBamAsBed0.080.000.08
readBedFile0.110.010.13
readFilesAsGRangesList 3.51 0.6610.81
saveGRangesAsBed0.130.000.12
saveGRangesAsTsv0.010.000.02
setGRGenomeInfo0.160.090.86