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This page was generated on 2022-04-13 12:07:20 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 segmentSeq on tokay2


To the developers/maintainers of the segmentSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1755/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.28.0  (landing page)
Thomas J. Hardcastle
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/segmentSeq
git_branch: RELEASE_3_14
git_last_commit: bc3e0b2
git_last_commit_date: 2021-10-26 11:55:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: segmentSeq
Version: 2.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmentSeq_2.28.0.tar.gz
StartedAt: 2022-04-13 02:40:20 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:48:45 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 504.9 seconds
RetCode: 0
Status:   OK  
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmentSeq_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/segmentSeq.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.28.0'
* 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 'segmentSeq' 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
* 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 ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
  'sDP'
Undefined global functions or variables:
  sDP
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
classifySeg     28.82   0.78   29.63
lociLikelihoods 12.97   0.00   12.99
heuristicSeg    12.60   0.00   12.59
plotGenome       6.85   0.00    6.85
normaliseNC      4.90   0.23    5.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
classifySeg     33.08   0.08   33.21
lociLikelihoods 16.23   0.00   16.24
heuristicSeg    15.41   0.01   15.47
plotGenome       8.37   0.02    8.39
getCounts        5.64   0.00    5.64
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.



Installation output

segmentSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/segmentSeq_2.28.0.tar.gz && rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmentSeq.buildbin-libdir segmentSeq_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL segmentSeq_2.28.0.zip && rm segmentSeq_2.28.0.tar.gz segmentSeq_2.28.0.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
 13 2360k   13  324k    0     0   957k      0  0:00:02 --:--:--  0:00:02  956k
100 2360k  100 2360k    0     0  1808k      0  0:00:01  0:00:01 --:--:-- 1809k

install for i386

* installing *source* package 'segmentSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'segmentSeq'
    finding HTML links ... done
    SL                                      html  
    alignmentClass-class                    html  
    alignmentData-class                     html  
    alignmentMeth-class                     html  
    averageMethylationRegions               html  
    finding level-2 HTML links ... done

    classifySeg                             html  
    findChunks                              html  
    getCounts                               html  
    getOverlaps                             html  
    givenExpression                         html  
    hSL                                     html  
    heuristicSeg                            html  
    lociData-class                          html  
    lociLikelihoods                         html  
    mergeMethSegs                           html  
    methData-class                          html  
    normaliseNC                             html  
    plotGenome                              html  
    plotMeth                                html  
    plotMethDistribution                    html  
    processAD                               html  
    readMethods                             html  
    readMeths                               html  
    segClass-class                          html  
    segData-class                           html  
    segMeth-class                           html  
    segmentSeq-package                      html  
    selectLoci                              html  
    summariseLoci                           html  
    thresholdFinder                         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 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.28.0.zip
* DONE (segmentSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'segmentSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

segmentSeq.Rcheck/examples_i386/segmentSeq-Ex.timings

nameusersystemelapsed
alignmentData-class3.540.033.67
classifySeg28.82 0.7829.63
findChunks2.970.002.97
getCounts4.750.004.75
getOverlaps3.010.003.02
heuristicSeg12.60 0.0012.59
lociLikelihoods12.97 0.0012.99
normaliseNC4.900.235.29
plotGenome6.850.006.85
processAD3.870.003.87
readMethods3.080.003.08
readMeths3.580.323.89
segData-class3.950.013.97
segmentSeq-package3.970.003.97
thresholdFinder2.770.283.05

segmentSeq.Rcheck/examples_x64/segmentSeq-Ex.timings

nameusersystemelapsed
alignmentData-class3.750.003.75
classifySeg33.08 0.0833.21
findChunks3.690.003.69
getCounts5.640.005.64
getOverlaps4.010.004.01
heuristicSeg15.41 0.0115.47
lociLikelihoods16.23 0.0016.24
normaliseNC3.740.284.01
plotGenome8.370.028.39
processAD4.560.004.57
readMethods3.600.003.59
readMeths3.620.343.97
segData-class4.470.004.47
segmentSeq-package4.580.024.59
thresholdFinder3.250.393.64