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CHECK report for MADSEQ on tokay2

This page was generated on 2019-10-16 12:36:02 -0400 (Wed, 16 Oct 2019).

Package 904/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MADSEQ 1.10.0
Yu Kong
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MADSEQ
Branch: RELEASE_3_9
Last Commit: b8dfd91
Last Changed Date: 2019-05-02 11:54:02 -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 [ OK ] 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: MADSEQ
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MADSEQ_1.10.0.tar.gz
StartedAt: 2019-10-16 04:53:13 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:00:05 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 412.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MADSEQ.Rcheck
Warnings: 0

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:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MADSEQ_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MADSEQ.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 'MADSEQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MADSEQ' version '1.10.0'
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCoverage 10.54   2.29   13.94
runMadSeq         11.14   0.07   11.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCoverage 10.46   1.09   11.56
runMadSeq         10.10   0.12   10.58
* 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-3.9-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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MADSEQ_1.10.0.tar.gz && rm -rf MADSEQ.buildbin-libdir && mkdir MADSEQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MADSEQ.buildbin-libdir MADSEQ_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MADSEQ_1.10.0.zip && rm MADSEQ_1.10.0.tar.gz MADSEQ_1.10.0.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
100 2126k  100 2126k    0     0  25.5M      0 --:--:-- --:--:-- --:--:-- 28.0M

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_1.10.0.zip
* DONE (MADSEQ)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MADSEQ' successfully unpacked and MD5 sums checked

Tests output


Example timings

MADSEQ.Rcheck/examples_i386/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.030.000.03
deltaBIC0.020.000.01
normalizeCoverage10.54 2.2913.94
plotFraction0.030.000.03
plotMadSeq0.050.000.04
plotMixture0.020.010.04
posterior0.140.140.28
prepareCoverageGC1.860.111.97
prepareHetero1.900.132.11
runMadSeq11.14 0.0711.39
summary-method0.010.000.02

MADSEQ.Rcheck/examples_x64/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr181.090.001.09
deltaBIC0.000.010.02
normalizeCoverage10.46 1.0911.56
plotFraction0.040.000.03
plotMadSeq0.030.000.03
plotMixture0.010.000.02
posterior0.190.080.27
prepareCoverageGC1.780.101.87
prepareHetero1.780.032.01
runMadSeq10.10 0.1210.58
summary-method0.010.020.03