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CHECK report for QDNAseq.mm10 on riesling1

This page was generated on 2021-01-14 15:59:11 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE QDNAseq.mm10 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 285/385HostnameOS / ArchINSTALLBUILDCHECK
QDNAseq.mm10 1.21.0
Daoud Sie
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/QDNAseq.mm10
Branch: master
Last Commit: 8ef5bae
Last Changed Date: 2020-10-27 10:14:43 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: QDNAseq.mm10
Version: 1.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.mm10.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QDNAseq.mm10_1.21.0.tar.gz
StartedAt: 2021-01-14 11:35:35 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:39:59 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 263.7 seconds
RetCode: 0
Status:  OK  
CheckDir: QDNAseq.mm10.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.mm10.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QDNAseq.mm10_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.mm10.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QDNAseq.mm10/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QDNAseq.mm10' version '1.21.0'
* 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 'QDNAseq.mm10' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 31.3Mb
  sub-directories of 1Mb or more:
    data  31.2Mb
* checking package 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
mm10.1kbp.SR50 12.86   0.22   13.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
mm10.1kbp.SR50 11.96   0.13   12.09
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.mm10.Rcheck/00check.log'
for details.



Installation output

QDNAseq.mm10.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/QDNAseq.mm10_1.21.0.tar.gz && rm -rf QDNAseq.mm10.buildbin-libdir && mkdir QDNAseq.mm10.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QDNAseq.mm10.buildbin-libdir QDNAseq.mm10_1.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL QDNAseq.mm10_1.21.0.zip && rm QDNAseq.mm10_1.21.0.tar.gz QDNAseq.mm10_1.21.0.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 31.1M  100 31.1M    0     0   107M      0 --:--:-- --:--:-- --:--:--  107M

install for i386

* installing *source* package 'QDNAseq.mm10' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QDNAseq.mm10'
    finding HTML links ... done
    QDNAseq.mm10-package                    html  
REDIRECT:topic	 QDNAseq.mm10-package -> QDNAseq.mm10-package.html [ SUCCESS ]
REDIRECT:topic	 QDNAseq.mm10 -> QDNAseq.mm10-package.html [ SUCCESS ]
    mm10.1000kbp.SR50                       html  
REDIRECT:topic	 mm10.1000kbp.SR50 -> mm10.1000kbp.SR50.html [ SUCCESS ]
    mm10.100kbp.SR50                        html  
REDIRECT:topic	 mm10.100kbp.SR50 -> mm10.100kbp.SR50.html [ SUCCESS ]
    mm10.10kbp.SR50                         html  
REDIRECT:topic	 mm10.10kbp.SR50 -> mm10.10kbp.SR50.html [ SUCCESS ]
    mm10.15kbp.SR50                         html  
REDIRECT:topic	 mm10.15kbp.SR50 -> mm10.15kbp.SR50.html [ SUCCESS ]
    mm10.1kbp.SR50                          html  
REDIRECT:topic	 mm10.1kbp.SR50 -> mm10.1kbp.SR50.html [ SUCCESS ]
    mm10.30kbp.SR50                         html  
REDIRECT:topic	 mm10.30kbp.SR50 -> mm10.30kbp.SR50.html [ SUCCESS ]
    mm10.500kbp.SR50                        html  
REDIRECT:topic	 mm10.500kbp.SR50 -> mm10.500kbp.SR50.html [ SUCCESS ]
    mm10.50kbp.SR50                         html  
REDIRECT:topic	 mm10.50kbp.SR50 -> mm10.50kbp.SR50.html [ SUCCESS ]
    mm10.5kbp.SR50                          html  
REDIRECT:topic	 mm10.5kbp.SR50 -> mm10.5kbp.SR50.html [ SUCCESS ]
** building package indices
** 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 'QDNAseq.mm10' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq.mm10' as QDNAseq.mm10_1.21.0.zip
* DONE (QDNAseq.mm10)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'QDNAseq.mm10' successfully unpacked and MD5 sums checked

Tests output


Example timings

QDNAseq.mm10.Rcheck/examples_i386/QDNAseq.mm10-Ex.timings

nameusersystemelapsed
QDNAseq.mm10-package0.360.000.36
mm10.1000kbp.SR500.020.020.03
mm10.100kbp.SR500.120.000.12
mm10.10kbp.SR501.330.021.34
mm10.15kbp.SR500.860.010.88
mm10.1kbp.SR5012.86 0.2213.08
mm10.30kbp.SR500.380.020.39
mm10.500kbp.SR500.030.000.03
mm10.50kbp.SR500.240.010.25
mm10.5kbp.SR502.750.142.89

QDNAseq.mm10.Rcheck/examples_x64/QDNAseq.mm10-Ex.timings

nameusersystemelapsed
QDNAseq.mm10-package0.390.000.39
mm10.1000kbp.SR500.020.010.03
mm10.100kbp.SR500.320.050.38
mm10.10kbp.SR501.190.031.21
mm10.15kbp.SR500.850.000.85
mm10.1kbp.SR5011.96 0.1312.09
mm10.30kbp.SR500.300.010.31
mm10.500kbp.SR500.000.030.04
mm10.50kbp.SR500.190.000.19
mm10.5kbp.SR501.670.081.75