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This page was generated on 2022-04-13 12:06:49 -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 MADSEQ on tokay2


To the developers/maintainers of the MADSEQ package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MADSEQ.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 1033/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MADSEQ 1.20.0  (landing page)
Yu Kong
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MADSEQ
git_branch: RELEASE_3_14
git_last_commit: 2665662
git_last_commit_date: 2021-10-26 12:28:19 -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: MADSEQ
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MADSEQ_1.20.0.tar.gz
StartedAt: 2022-04-12 22:09:00 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:16:06 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 426.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MADSEQ.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:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MADSEQ_1.20.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MADSEQ.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 'MADSEQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MADSEQ' version '1.20.0'
* 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 'MADSEQ' 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
removeRE: no visible global function definition for 'seqlevelsStyle<-'
Undefined global functions or variables:
  seqlevelsStyle<-
* 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 ... 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
normalizeCoverage 11.91   1.82   14.55
runMadSeq         10.62   0.11   11.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
normalizeCoverage 11.43   1.01   12.44
runMadSeq          7.91   0.08    8.18
* 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/MADSEQ.Rcheck/00check.log'
for details.



Installation output

MADSEQ.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/MADSEQ_1.20.0.tar.gz && rm -rf MADSEQ.buildbin-libdir && mkdir MADSEQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MADSEQ.buildbin-libdir MADSEQ_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MADSEQ_1.20.0.zip && rm MADSEQ_1.20.0.tar.gz MADSEQ_1.20.0.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
  3 1872k    3 74113    0     0   378k      0  0:00:04 --:--:--  0:00:04  378k
 69 1872k   69 1308k    0     0  1098k      0  0:00:01  0:00:01 --:--:-- 1098k
100 1872k  100 1872k    0     0  1257k      0  0:00:01  0:00:01 --:--:-- 1257k

install for i386

* installing *source* package 'MADSEQ' ...
** 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 'MADSEQ'
    finding HTML links ... done
    MADSEQ-package                          html  
    MadSeq                                  html  
    aneuploidy_chr18                        html  
    deltaBIC                                html  
    normalizeCoverage                       html  
    finding level-2 HTML links ... done

    plotFraction                            html  
    plotMadSeq                              html  
    plotMixture                             html  
    posterior                               html  
    prepareCoverageGC                       html  
    prepareHetero                           html  
    runMadSeq                               html  
    summary-method                          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 'MADSEQ' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MADSEQ' as MADSEQ_1.20.0.zip
* DONE (MADSEQ)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MADSEQ' successfully unpacked and MD5 sums checked

Tests output


Example timings

MADSEQ.Rcheck/examples_i386/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.050.000.04
deltaBIC0.010.000.02
normalizeCoverage11.91 1.8214.55
plotFraction0.030.000.03
plotMadSeq0.070.010.08
plotMixture0.030.020.05
posterior0.340.090.44
prepareCoverageGC1.800.091.89
prepareHetero2.050.072.98
runMadSeq10.62 0.1111.31
summary-method0.030.000.03

MADSEQ.Rcheck/examples_x64/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.010.000.02
deltaBIC000
normalizeCoverage11.43 1.0112.44
plotFraction0.020.000.02
plotMadSeq0.030.000.03
plotMixture0.010.020.03
posterior0.190.090.28
prepareCoverageGC1.770.171.94
prepareHetero2.250.052.47
runMadSeq7.910.088.18
summary-method0.000.010.01