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CHECK report for QDNAseq.hg19 on riesling1

This page was generated on 2021-01-21 16:01:35 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE QDNAseq.hg19 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 284/386HostnameOS / ArchINSTALLBUILDCHECK
QDNAseq.hg19 1.21.0
Daoud Sie
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/QDNAseq.hg19
Branch: master
Last Commit: ee8d568
Last Changed Date: 2020-10-27 10:14:40 -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.hg19
Version: 1.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.hg19.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QDNAseq.hg19_1.21.0.tar.gz
StartedAt: 2021-01-21 11:41:21 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:43:53 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 151.6 seconds
RetCode: 0
Status:  OK  
CheckDir: QDNAseq.hg19.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.hg19.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QDNAseq.hg19_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.hg19.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.hg19/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QDNAseq.hg19' 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.hg19' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.4Mb
  sub-directories of 1Mb or more:
    data  35.3Mb
* 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
hg19.1kbp.SR50 14.01   0.23   14.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
hg19.1kbp.SR50 13.3   0.19   13.49
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.hg19.Rcheck/00check.log'
for details.



Installation output

QDNAseq.hg19.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.hg19_1.21.0.tar.gz && rm -rf QDNAseq.hg19.buildbin-libdir && mkdir QDNAseq.hg19.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QDNAseq.hg19.buildbin-libdir QDNAseq.hg19_1.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL QDNAseq.hg19_1.21.0.zip && rm QDNAseq.hg19_1.21.0.tar.gz QDNAseq.hg19_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
  0 35.2M    0  172k    0     0  1596k      0  0:00:22 --:--:--  0:00:22 1582k
100 35.2M  100 35.2M    0     0  42.6M      0 --:--:-- --:--:-- --:--:-- 42.5M

install for i386

* installing *source* package 'QDNAseq.hg19' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QDNAseq.hg19'
    finding HTML links ... done
    QDNAseq.hg19-package                    html  
REDIRECT:topic	 QDNAseq.hg19-package -> QDNAseq.hg19-package.html [ SUCCESS ]
REDIRECT:topic	 QDNAseq.hg19 -> QDNAseq.hg19-package.html [ SUCCESS ]
    hg19.1000kbp.SR50                       html  
REDIRECT:topic	 hg19.1000kbp.SR50 -> hg19.1000kbp.SR50.html [ SUCCESS ]
    hg19.100kbp.SR50                        html  
REDIRECT:topic	 hg19.100kbp.SR50 -> hg19.100kbp.SR50.html [ SUCCESS ]
    hg19.10kbp.SR50                         html  
REDIRECT:topic	 hg19.10kbp.SR50 -> hg19.10kbp.SR50.html [ SUCCESS ]
    hg19.15kbp.SR50                         html  
REDIRECT:topic	 hg19.15kbp.SR50 -> hg19.15kbp.SR50.html [ SUCCESS ]
    hg19.1kbp.SR50                          html  
REDIRECT:topic	 hg19.1kbp.SR50 -> hg19.1kbp.SR50.html [ SUCCESS ]
    hg19.30kbp.SR50                         html  
REDIRECT:topic	 hg19.30kbp.SR50 -> hg19.30kbp.SR50.html [ SUCCESS ]
    hg19.500kbp.SR50                        html  
REDIRECT:topic	 hg19.500kbp.SR50 -> hg19.500kbp.SR50.html [ SUCCESS ]
    hg19.50kbp.SR50                         html  
REDIRECT:topic	 hg19.50kbp.SR50 -> hg19.50kbp.SR50.html [ SUCCESS ]
    hg19.5kbp.SR50                          html  
REDIRECT:topic	 hg19.5kbp.SR50 -> hg19.5kbp.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.hg19' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq.hg19' as QDNAseq.hg19_1.21.0.zip
* DONE (QDNAseq.hg19)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'QDNAseq.hg19' successfully unpacked and MD5 sums checked

Tests output


Example timings

QDNAseq.hg19.Rcheck/examples_i386/QDNAseq.hg19-Ex.timings

nameusersystemelapsed
QDNAseq.hg19-package0.380.030.41
hg19.1000kbp.SR500.030.000.03
hg19.100kbp.SR500.140.020.16
hg19.10kbp.SR501.640.081.72
hg19.15kbp.SR501.220.031.25
hg19.1kbp.SR5014.01 0.2314.25
hg19.30kbp.SR500.410.020.42
hg19.500kbp.SR500.030.000.03
hg19.50kbp.SR500.240.030.27
hg19.5kbp.SR503.220.173.39

QDNAseq.hg19.Rcheck/examples_x64/QDNAseq.hg19-Ex.timings

nameusersystemelapsed
QDNAseq.hg19-package0.660.000.66
hg19.1000kbp.SR500.000.010.01
hg19.100kbp.SR500.120.000.12
hg19.10kbp.SR501.190.101.28
hg19.15kbp.SR500.840.010.85
hg19.1kbp.SR5013.30 0.1913.49
hg19.30kbp.SR500.330.030.36
hg19.500kbp.SR500.030.000.03
hg19.50kbp.SR500.220.000.22
hg19.5kbp.SR502.170.092.27