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This page was generated on 2022-01-21 13:06:27 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for gscreend on tokay2


To the developers/maintainers of the gscreend package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gscreend.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 831/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gscreend 1.8.0  (landing page)
Katharina Imkeller
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/gscreend
git_branch: RELEASE_3_14
git_last_commit: 56f9c2a
git_last_commit_date: 2021-10-26 12:55:02 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: gscreend
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gscreend.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gscreend_1.8.0.tar.gz
StartedAt: 2022-01-20 21:02:08 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 21:11:53 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 585.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gscreend.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gscreend.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gscreend_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gscreend.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gscreend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gscreend' version '1.8.0'
* 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 'gscreend' 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
RunGscreend 73.67  15.41  171.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
RunGscreend 75.46  15.93   194.9
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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

gscreend.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/gscreend_1.8.0.tar.gz && rm -rf gscreend.buildbin-libdir && mkdir gscreend.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gscreend.buildbin-libdir gscreend_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL gscreend_1.8.0.zip && rm gscreend_1.8.0.tar.gz gscreend_1.8.0.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
 12 2906k   12  349k    0     0  1044k      0  0:00:02 --:--:--  0:00:02 1042k
 90 2906k   90 2639k    0     0  2002k      0  0:00:01  0:00:01 --:--:-- 2002k
100 2906k  100 2906k    0     0  2039k      0  0:00:01  0:00:01 --:--:-- 2039k

install for i386

* installing *source* package 'gscreend' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gscreend'
    finding HTML links ... done
    GeneData-PoolScreenExp-method           html  
    GeneData                                html  
    PoolScreenExp-class                     html  
    ResultsTable                            html  
    RunGscreend                             html  
    assignGeneData                          html  
    calculateIntervalFits                   html  
    calculateLFC                            html  
    calculatePValues                        html  
    createPoolScreenExp                     html  
    createPoolScreenExpFromSE               html  
    defineFittingIntervals                  html  
    fit_least_quantile                      html  
    normalizePoolScreenExp                  html  
    plotModelParameters                     html  
    plotReplicateCorrelation                html  
    sgRNAData-PoolScreenExp-method          html  
    sgRNAData                               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 'gscreend' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gscreend' as gscreend_1.8.0.zip
* DONE (gscreend)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'gscreend' successfully unpacked and MD5 sums checked

Tests output

gscreend.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gscreend)
> 
> test_check("gscreend")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   8.03    0.71    9.71 

gscreend.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gscreend)
> 
> test_check("gscreend")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   6.93    0.39    7.31 

Example timings

gscreend.Rcheck/examples_i386/gscreend-Ex.timings

nameusersystemelapsed
GeneData-PoolScreenExp-method0.310.020.38
GeneData0.170.000.18
ResultsTable0.530.070.61
RunGscreend 73.67 15.41171.36
createPoolScreenExp0.370.030.41
plotModelParameters0.190.020.20
plotReplicateCorrelation1.410.011.42
sgRNAData-PoolScreenExp-method0.140.000.14
sgRNAData0.190.000.19

gscreend.Rcheck/examples_x64/gscreend-Ex.timings

nameusersystemelapsed
GeneData-PoolScreenExp-method0.590.040.62
GeneData0.110.000.11
ResultsTable0.390.110.50
RunGscreend 75.46 15.93194.90
createPoolScreenExp0.230.020.25
plotModelParameters0.110.000.11
plotReplicateCorrelation0.890.010.91
sgRNAData-PoolScreenExp-method0.080.020.09
sgRNAData0.090.000.10