Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:18:04 -0500 (Wed, 01 Dec 2021).

CHECK results for scmeth on tokay2

To the developers/maintainers of the scmeth package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scmeth.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 1731/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scmeth 1.14.0  (landing page)
Divy Kangeyan
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/scmeth
git_branch: RELEASE_3_14
git_last_commit: cb59e2c
git_last_commit_date: 2021-10-26 12:41:54 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: scmeth
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scmeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scmeth_1.14.0.tar.gz
StartedAt: 2021-12-01 05:11:14 -0500 (Wed, 01 Dec 2021)
EndedAt: 2021-12-01 05:20:01 -0500 (Wed, 01 Dec 2021)
EllapsedTime: 527.2 seconds
RetCode: 0
Status:   OK  
CheckDir: scmeth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scmeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scmeth_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scmeth.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scmeth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scmeth' version '1.14.0'
* 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 'scmeth' 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 ... NOTE
Namespace in Imports field not imported from: 'reshape2'
  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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
report  51.90   3.00   56.12
repMask 19.22   3.58   24.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
report  46.81   2.24   50.50
repMask 15.64   0.69   17.64
* 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/scmeth.Rcheck/00check.log'
for details.



Installation output

scmeth.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scmeth_1.14.0.tar.gz && rm -rf scmeth.buildbin-libdir && mkdir scmeth.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scmeth.buildbin-libdir scmeth_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scmeth_1.14.0.zip && rm scmeth_1.14.0.tar.gz scmeth_1.14.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2  733k    2 16227    0     0  14138      0  0:00:53  0:00:01  0:00:52 14147
 22  733k   22  162k    0     0  67871      0  0:00:11  0:00:02  0:00:09 67897
 22  733k   22  162k    0     0  47964      0  0:00:15  0:00:03  0:00:12 47971
 23  733k   23  169k    0     0  44832      0  0:00:16  0:00:03  0:00:13 44830
 49  733k   49  365k    0     0  75358      0  0:00:09  0:00:04  0:00:05 75353
 49  733k   49  365k    0     0  62556      0  0:00:12  0:00:05  0:00:07 74052
 51  733k   51  375k    0     0  55526      0  0:00:13  0:00:06  0:00:07 48784
 67  733k   67  492k    0     0  63244      0  0:00:11  0:00:07  0:00:04 74960
 67  733k   67  492k    0     0  56103      0  0:00:13  0:00:08  0:00:05 64668
 71  733k   71  524k    0     0  52801      0  0:00:14  0:00:10  0:00:04 31356
 71  733k   71  524k    0     0  48011      0  0:00:15  0:00:11  0:00:04 31350
 71  733k   71  524k    0     0  44018      0  0:00:17  0:00:12  0:00:05 28926
 71  733k   71  524k    0     0  40639      0  0:00:18  0:00:13  0:00:05  6285
100  733k  100  733k    0     0  55704      0  0:00:13  0:00:13 --:--:-- 54916

install for i386

* installing *source* package 'scmeth' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scmeth'
    finding HTML links ... done
    bsConversionPlot                        html  
    chromosomeCoverage                      html  
    coverage                                html  
    cpgDensity                              html  
    cpgDiscretization                       html  
    downsample                              html  
    featureCoverage                         html  
    mbiasplot                               html  
    methylationDist                         html  
    readmetrics                             html  
    repMask                                 html  
    report                                  html  
    scmeth                                  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 'scmeth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scmeth' as scmeth_1.14.0.zip
* DONE (scmeth)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scmeth' successfully unpacked and MD5 sums checked

Tests output


Example timings

scmeth.Rcheck/examples_i386/scmeth-Ex.timings

nameusersystemelapsed
bsConversionPlot0.300.060.40
chromosomeCoverage0.530.260.80
coverage0.140.020.16
cpgDensity3.410.303.70
cpgDiscretization0.230.060.31
downsample1.500.081.58
featureCoverage2.800.594.24
mbiasplot0.010.000.03
methylationDist0.220.000.22
readmetrics0.100.000.09
repMask19.22 3.5824.30
report51.90 3.0056.12

scmeth.Rcheck/examples_x64/scmeth-Ex.timings

nameusersystemelapsed
bsConversionPlot0.200.000.21
chromosomeCoverage1.280.031.31
coverage0.120.010.14
cpgDensity3.380.193.56
cpgDiscretization0.250.020.26
downsample0.430.030.47
featureCoverage3.380.144.44
mbiasplot000
methylationDist0.160.000.16
readmetrics0.050.010.06
repMask15.64 0.6917.64
report46.81 2.2450.50