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CHECK report for SCATEData on riesling1

This page was generated on 2021-01-21 16:01:38 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SCATEData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 322/386HostnameOS / ArchINSTALLBUILDCHECK
SCATEData 1.1.0
Wenpin Hou
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/SCATEData
Branch: master
Last Commit: 21918ad
Last Changed Date: 2020-10-27 10:32:09 -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: SCATEData
Version: 1.1.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCATEData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SCATEData_1.1.0.tar.gz
StartedAt: 2021-01-21 11:46:11 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:50:15 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 243.8 seconds
RetCode: 0
Status:  OK  
CheckDir: SCATEData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCATEData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SCATEData_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/SCATEData.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 'SCATEData/DESCRIPTION' ... OK
* this is package 'SCATEData' version '1.1.0'
* package encoding: UTF-8
* 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 'SCATEData' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 190.1Mb
  sub-directories of 1Mb or more:
    extdata  189.9Mb
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: hg19.rds.Rd:18-19: Dropping empty section \usage
prepare_Rd: mm10.rds.Rd:18-19: Dropping empty section \usage
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
hg19.rds 7.93   0.14    8.08
mm10.rds 5.74   0.20    5.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
hg19.rds  6.8   0.14    6.94
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/SCATEData.Rcheck/00check.log'
for details.



Installation output

SCATEData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/SCATEData_1.1.0.tar.gz && rm -rf SCATEData.buildbin-libdir && mkdir SCATEData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCATEData.buildbin-libdir SCATEData_1.1.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SCATEData_1.1.0.zip && rm SCATEData_1.1.0.tar.gz SCATEData_1.1.0.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
 39  159M   39 63.3M    0     0  71.7M      0  0:00:02 --:--:--  0:00:02 71.7M
100  159M  100  159M    0     0  92.0M      0  0:00:01  0:00:01 --:--:-- 92.0M

install for i386

* installing *source* package 'SCATEData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SCATEData'
    finding HTML links ... done
    GSM1596831.bam                          html  
REDIRECT:topic	 GSM1596831.bam -> GSM1596831.bam.html [ SUCCESS ]
    GSM1596840.bam                          html  
REDIRECT:topic	 GSM1596840.bam -> GSM1596840.bam.html [ SUCCESS ]
    GSM1596874.bam                          html  
REDIRECT:topic	 GSM1596874.bam -> GSM1596874.bam.html [ SUCCESS ]
    GSM1596881.bam                          html  
REDIRECT:topic	 GSM1596881.bam -> GSM1596881.bam.html [ SUCCESS ]
    GSM1596940.bam                          html  
REDIRECT:topic	 GSM1596940.bam -> GSM1596940.bam.html [ SUCCESS ]
    GSM1596942.bam                          html  
REDIRECT:topic	 GSM1596942.bam -> GSM1596942.bam.html [ SUCCESS ]
    GSM1596944.bam                          html  
REDIRECT:topic	 GSM1596944.bam -> GSM1596944.bam.html [ SUCCESS ]
    GSM1596961.bam                          html  
REDIRECT:topic	 GSM1596961.bam -> GSM1596961.bam.html [ SUCCESS ]
    GSM1597041.bam                          html  
REDIRECT:topic	 GSM1597041.bam -> GSM1597041.bam.html [ SUCCESS ]
    GSM1597096.bam                          html  
REDIRECT:topic	 GSM1597096.bam -> GSM1597096.bam.html [ SUCCESS ]
    SCATEData-package                       html  
REDIRECT:topic	 SCATEData -> SCATEData-package.html [ SUCCESS ]
REDIRECT:topic	 SCATEData-package -> SCATEData-package.html [ SUCCESS ]
    finding level-2 HTML links ... done

    SRR1779746.bam                          html  
REDIRECT:topic	 SRR1779746.bam -> SRR1779746.bam.html [ SUCCESS ]
    SRR1779805.bam                          html  
REDIRECT:topic	 SRR1779805.bam -> SRR1779805.bam.html [ SUCCESS ]
    SRR1779856.bam                          html  
REDIRECT:topic	 SRR1779856.bam -> SRR1779856.bam.html [ SUCCESS ]
    SRR1779874.bam                          html  
REDIRECT:topic	 SRR1779874.bam -> SRR1779874.bam.html [ SUCCESS ]
    SRR1779956.bam                          html  
REDIRECT:topic	 SRR1779956.bam -> SRR1779956.bam.html [ SUCCESS ]
    SRR1779959.bam                          html  
REDIRECT:topic	 SRR1779959.bam -> SRR1779959.bam.html [ SUCCESS ]
    SRR1779973.bam                          html  
REDIRECT:topic	 SRR1779973.bam -> SRR1779973.bam.html [ SUCCESS ]
    SRR1780018.bam                          html  
REDIRECT:topic	 SRR1780018.bam -> SRR1780018.bam.html [ SUCCESS ]
    SRR1780020.bam                          html  
REDIRECT:topic	 SRR1780020.bam -> SRR1780020.bam.html [ SUCCESS ]
    SRR1780054.bam                          html  
REDIRECT:topic	 SRR1780054.bam -> SRR1780054.bam.html [ SUCCESS ]
    hg19.rds                                html  
REDIRECT:topic	 hg19.rds -> hg19.rds.html [ SUCCESS ]
REDIRECT:topic	 hg19 annotation file -> hg19.rds.html [ SUCCESS ]
    mm10.rds                                html  
REDIRECT:topic	 mm10.rds -> mm10.rds.html [ SUCCESS ]
REDIRECT:topic	 mm10 annotation file -> mm10.rds.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-20
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-20
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SCATEData' ...
** testing if installed package can be loaded
snapshotDate(): 2021-01-20
* MD5 sums
packaged installation of 'SCATEData' as SCATEData_1.1.0.zip
* DONE (SCATEData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'SCATEData' successfully unpacked and MD5 sums checked

Tests output


Example timings

SCATEData.Rcheck/examples_i386/SCATEData-Ex.timings

nameusersystemelapsed
GSM1596831.bam0.050.000.05
GSM1596840.bam0.050.020.06
GSM1596874.bam0.030.000.03
GSM1596881.bam0.050.000.04
GSM1596940.bam0.020.000.02
GSM1596942.bam0.030.000.03
GSM1596944.bam0.050.000.04
GSM1596961.bam0.060.000.06
GSM1597041.bam0.050.000.04
GSM1597096.bam0.050.000.05
SRR1779746.bam0.040.010.06
SRR1779805.bam0.100.000.09
SRR1779856.bam0.010.000.02
SRR1779874.bam0.10.00.1
SRR1779956.bam0.040.020.06
SRR1779959.bam0.060.000.06
SRR1779973.bam0.050.000.04
SRR1780018.bam0.010.000.02
SRR1780020.bam0.050.000.05
SRR1780054.bam0.100.000.09
hg19.rds7.930.148.08
mm10.rds5.740.205.94

SCATEData.Rcheck/examples_x64/SCATEData-Ex.timings

nameusersystemelapsed
GSM1596831.bam0.040.000.04
GSM1596840.bam0.050.000.04
GSM1596874.bam0.040.000.03
GSM1596881.bam0.040.000.05
GSM1596940.bam0.020.000.01
GSM1596942.bam0.030.000.04
GSM1596944.bam0.060.000.06
GSM1596961.bam0.080.000.08
GSM1597041.bam0.060.000.06
GSM1597096.bam0.050.000.05
SRR1779746.bam0.080.010.09
SRR1779805.bam0.080.000.08
SRR1779856.bam0.010.000.01
SRR1779874.bam0.100.000.09
SRR1779956.bam0.040.020.07
SRR1779959.bam0.060.000.06
SRR1779973.bam0.050.000.05
SRR1780018.bam0.020.000.02
SRR1780020.bam0.040.000.04
SRR1780054.bam0.550.000.55
hg19.rds6.800.146.94
mm10.rds4.390.174.56