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This page was generated on 2021-09-22 15:05:14 -0400 (Wed, 22 Sep 2021).

CHECK results for FilterFFPE on tokay2

To the developers/maintainers of the FilterFFPE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FilterFFPE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 633/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FilterFFPE 1.2.0  (landing page)
Lanying Wei
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/FilterFFPE
git_branch: RELEASE_3_13
git_last_commit: 567bb26
git_last_commit_date: 2021-05-19 12:55:31 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FilterFFPE
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FilterFFPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FilterFFPE_1.2.0.tar.gz
StartedAt: 2021-09-21 22:47:05 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 22:52:30 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 324.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FilterFFPE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FilterFFPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FilterFFPE_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/FilterFFPE.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FilterFFPE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FilterFFPE' version '1.2.0'
* 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 'FilterFFPE' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
FFPEReadFilter            1.31   0.12   26.31
FilterFFPE-package        1.27   0.06   24.74
filterBamByReadNames      1.17   0.05   24.94
findArtifactChimericReads 0.58   0.00   23.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
FFPEReadFilter            1.36   0.13   25.80
FilterFFPE-package        1.36   0.07   25.33
filterBamByReadNames      1.13   0.14   25.81
findArtifactChimericReads 0.70   0.08   25.18
* 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: OK


Installation output

FilterFFPE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FilterFFPE_1.2.0.tar.gz && rm -rf FilterFFPE.buildbin-libdir && mkdir FilterFFPE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FilterFFPE.buildbin-libdir FilterFFPE_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FilterFFPE_1.2.0.zip && rm FilterFFPE_1.2.0.tar.gz FilterFFPE_1.2.0.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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1191k  100 1191k    0     0  1877k      0 --:--:-- --:--:-- --:--:-- 1878k

install for i386

* installing *source* package 'FilterFFPE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FilterFFPE'
    finding HTML links ... done
    FFPEReadFilter                          html  
    FilterFFPE-package                      html  
    filterBamByReadNames                    html  
    findArtifactChimericReads               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 'FilterFFPE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FilterFFPE' as FilterFFPE_1.2.0.zip
* DONE (FilterFFPE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'FilterFFPE' successfully unpacked and MD5 sums checked

Tests output


Example timings

FilterFFPE.Rcheck/examples_i386/FilterFFPE-Ex.timings

nameusersystemelapsed
FFPEReadFilter 1.31 0.1226.31
FilterFFPE-package 1.27 0.0624.74
filterBamByReadNames 1.17 0.0524.94
findArtifactChimericReads 0.58 0.0023.26

FilterFFPE.Rcheck/examples_x64/FilterFFPE-Ex.timings

nameusersystemelapsed
FFPEReadFilter 1.36 0.1325.80
FilterFFPE-package 1.36 0.0725.33
filterBamByReadNames 1.13 0.1425.81
findArtifactChimericReads 0.70 0.0825.18