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CHECK report for ELBOW on tokay1

This page was generated on 2021-05-06 12:31:02 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ELBOW package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 540/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELBOW 1.26.0  (landing page)
Graham Alvare , Xiangli Zhang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ELBOW
Branch: RELEASE_3_12
Last Commit: 40d6a67
Last Changed Date: 2020-10-27 10:54:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ELBOW
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELBOW.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ELBOW_1.26.0.tar.gz
StartedAt: 2021-05-06 02:30:34 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:31:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 55.7 seconds
RetCode: 0
Status:   OK   
CheckDir: ELBOW.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELBOW.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ELBOW_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ELBOW.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ELBOW/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ELBOW' version '1.26.0'
* 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 'ELBOW' 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 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 (user + system) or elapsed time > 5s
                user system elapsed
do_elbow_rnaseq 6.31   0.27     6.6
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
do_elbow_rnaseq 6.97   0.19    7.21
* 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

ELBOW.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ELBOW_1.26.0.tar.gz && rm -rf ELBOW.buildbin-libdir && mkdir ELBOW.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ELBOW.buildbin-libdir ELBOW_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ELBOW_1.26.0.zip && rm ELBOW_1.26.0.tar.gz ELBOW_1.26.0.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 1112k  100 1112k    0     0  40.8M      0 --:--:-- --:--:-- --:--:-- 41.7M

install for i386

* installing *source* package 'ELBOW' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ELBOW'
    finding HTML links ... done
    ELBOW-package                           html  
    EcoliMutMA                              html  
    EcoliWT                                 html  
    GSE20986_design                         html  
    GSE20986_eset_exprs                     html  
    analyze_elbow                           html  
    do_elbow                                html  
    do_elbow_rnaseq                         html  
    elbow_variance                          html  
    extract_working_sets                    html  
    get_elbow_limma                         html  
    get_pvalue                              html  
    null_variance                           html  
    plot_dataset                            html  
    plot_elbow                              html  
    replicates_to_fold                      html  
    yeast_nbinomTest_results                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 'ELBOW' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ELBOW' as ELBOW_1.26.0.zip
* DONE (ELBOW)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ELBOW' successfully unpacked and MD5 sums checked

Tests output


Example timings

ELBOW.Rcheck/examples_i386/ELBOW-Ex.timings

nameusersystemelapsed
ELBOW-package1.210.041.27
analyze_elbow1.250.031.28
do_elbow0.110.000.11
do_elbow_rnaseq6.310.276.60
elbow_variance0.630.000.62
extract_working_sets0.040.000.05
get_elbow_limma0.470.000.47
get_pvalue1.240.031.26
null_variance0.920.000.92
plot_dataset0.840.020.93
plot_elbow1.240.011.26
replicates_to_fold0.080.000.11

ELBOW.Rcheck/examples_x64/ELBOW-Ex.timings

nameusersystemelapsed
ELBOW-package1.200.041.26
analyze_elbow1.250.001.25
do_elbow0.110.000.11
do_elbow_rnaseq6.970.197.21
elbow_variance0.960.000.95
extract_working_sets0.060.000.06
get_elbow_limma0.470.000.47
get_pvalue0.980.021.00
null_variance0.860.010.88
plot_dataset0.810.050.86
plot_elbow1.170.001.17
replicates_to_fold0.080.000.08