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CHECK report for MADSEQ on tokay1

This page was generated on 2019-04-13 11:26:47 -0400 (Sat, 13 Apr 2019).

Package 865/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MADSEQ 1.8.0
Yu Kong
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MADSEQ
Branch: RELEASE_3_8
Last Commit: df64e91
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MADSEQ
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MADSEQ_1.8.0.tar.gz
StartedAt: 2019-04-13 03:29:35 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:36:10 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 394.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MADSEQ.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MADSEQ_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MADSEQ.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
runMadSeq         10.06   0.09   10.82
normalizeCoverage  7.56   1.19    9.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeCoverage 9.97   0.72   10.74
runMadSeq         8.12   0.13    8.25
* 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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MADSEQ_1.8.0.tar.gz && rm -rf MADSEQ.buildbin-libdir && mkdir MADSEQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MADSEQ.buildbin-libdir MADSEQ_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MADSEQ_1.8.0.zip && rm MADSEQ_1.8.0.tar.gz MADSEQ_1.8.0.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
  0 2122k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2122k  100 2122k    0     0  12.2M      0 --:--:-- --:--:-- --:--:-- 12.4M

install for i386

* installing *source* package 'MADSEQ' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'MADSEQ' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MADSEQ' as MADSEQ_1.8.0.zip
* DONE (MADSEQ)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MADSEQ' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

MADSEQ.Rcheck/examples_i386/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.010.020.03
deltaBIC0.020.000.01
normalizeCoverage7.561.199.38
plotFraction0.020.000.02
plotMadSeq0.050.000.05
plotMixture0.010.010.03
posterior0.140.140.28
prepareCoverageGC1.330.141.47
prepareHetero1.190.171.53
runMadSeq10.06 0.0910.82
summary-method0.030.000.03

MADSEQ.Rcheck/examples_x64/MADSEQ-Ex.timings

nameusersystemelapsed
aneuploidy_chr180.030.000.03
deltaBIC000
normalizeCoverage 9.97 0.7210.74
plotFraction0.020.010.03
plotMadSeq0.040.000.05
plotMixture0.030.000.03
posterior0.220.110.33
prepareCoverageGC2.080.072.14
prepareHetero1.500.071.57
runMadSeq8.120.138.25
summary-method0.010.000.02