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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).

CHECK results for BaalChIP on tokay2

To the developers/maintainers of the BaalChIP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BaalChIP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 106/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaalChIP 1.18.0  (landing page)
Ines de Santiago
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/BaalChIP
git_branch: RELEASE_3_13
git_last_commit: 49e2ae7
git_last_commit_date: 2021-05-19 12:22:59 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BaalChIP
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaalChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BaalChIP_1.18.0.tar.gz
StartedAt: 2021-10-14 19:44:33 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:02:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 1084.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BaalChIP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaalChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BaalChIP_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BaalChIP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BaalChIP/DESCRIPTION' ... OK
* this is package 'BaalChIP' version '1.18.0'
* 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 'BaalChIP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 198.3Mb
  sub-directories of 1Mb or more:
    data   95.8Mb
    test  101.9Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 95.7 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
BaalChIP.run  18.52   1.61  156.75
mergePerGroup 11.06   1.29   12.36
QCfilter      10.37   1.68   12.06
filter1allele  9.61   1.17   10.78
filterIntbias  6.97   0.10   12.74
getASB         5.55   0.58  153.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
BaalChIP.run  16.89   1.67  157.47
mergePerGroup 12.92   1.36   14.29
QCfilter      11.01   1.35   12.35
filter1allele 10.08   1.39   11.47
getASB         6.53   0.42  161.95
filterIntbias  6.36   0.21    6.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BaalChIP.Rcheck/00check.log'
for details.

Installation output

BaalChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BaalChIP_1.18.0.tar.gz && rm -rf BaalChIP.buildbin-libdir && mkdir BaalChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BaalChIP.buildbin-libdir BaalChIP_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BaalChIP_1.18.0.zip && rm BaalChIP_1.18.0.tar.gz BaalChIP_1.18.0.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
  0 44.3M    0   98k    0     0   516k      0  0:01:27 --:--:--  0:01:27  515k
  9 44.3M    9 4216k    0     0  3551k      0  0:00:12  0:00:01  0:00:11 3551k
 21 44.3M   21 9633k    0     0  4444k      0  0:00:10  0:00:02  0:00:08 4445k
 34 44.3M   34 15.1M    0     0  4860k      0  0:00:09  0:00:03  0:00:06 4860k
 49 44.3M   49 21.9M    0     0  5407k      0  0:00:08  0:00:04  0:00:04 5408k
 66 44.3M   66 29.7M    0     0  5881k      0  0:00:07  0:00:05  0:00:02 6087k
 82 44.3M   82 36.6M    0     0  6070k      0  0:00:07  0:00:06  0:00:01 6668k
100 44.3M  100 44.3M    0     0  6402k      0  0:00:07  0:00:07 --:--:-- 7265k

install for i386

* installing *source* package 'BaalChIP' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BaalChIP'
    finding HTML links ... done
    BaalChIP                                html  
    BaalChIP.get                            html  
    BaalChIP.report                         html  
    BaalChIP.run                            html  
    BaalObject                              html  
    ENCODEexample                           html  
    FAIREexample                            html  
    QCfilter                                html  
    UniqueMappability50bp_hg19              html  
    adjustmentBaalPlot                      html  
    alleleCounts                            html  
    blacklist_hg19                          html  
    filter1allele                           html  
    filterIntbias                           html  
    getASB                                  html  
    mergePerGroup                           html  
    pickrell2011cov1_hg19                   html  
    plotQC                                  html  
    plotSimul                               html  
    summaryASB                              html  
    summaryQC                               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 'BaalChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BaalChIP' as BaalChIP_1.18.0.zip
* DONE (BaalChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BaalChIP' successfully unpacked and MD5 sums checked

Tests output

BaalChIP.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("BaalChIP")

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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Thu Oct 14 20:02:19 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BaalChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   8.10    0.84    8.93

BaalChIP.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> BiocGenerics:::testPackage("BaalChIP")

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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Thu Oct 14 20:02:29 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BaalChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   8.57    0.35    8.92

Example timings

BaalChIP.Rcheck/examples_i386/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP0.030.000.04
BaalChIP.get0.080.000.07
BaalChIP.report0.010.020.03
BaalChIP.run 18.52 1.61156.75
QCfilter10.37 1.6812.06
adjustmentBaalPlot0.520.000.52
alleleCounts2.980.083.06
filter1allele 9.61 1.1710.78
filterIntbias 6.97 0.1012.74
getASB 5.55 0.58153.59
mergePerGroup11.06 1.2912.36
plotQC0.750.030.78
plotSimul0.130.000.13
summaryASB0.000.020.01
summaryQC0.040.000.05

BaalChIP.Rcheck/examples_x64/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP0.030.000.03
BaalChIP.get0.10.00.1
BaalChIP.report0.020.000.02
BaalChIP.run 16.89 1.67157.47
QCfilter11.01 1.3512.35
adjustmentBaalPlot0.570.010.58
alleleCounts3.430.003.44
filter1allele10.08 1.3911.47
filterIntbias6.360.216.56
getASB 6.53 0.42161.95
mergePerGroup12.92 1.3614.29
plotQC0.790.030.81
plotSimul0.100.010.12
summaryASB000
summaryQC0.050.000.05