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This page was generated on 2022-06-30 11:06:51 -0400 (Thu, 30 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4147
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
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 MPRAnalyze on palomino4


To the developers/maintainers of the MPRAnalyze package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MPRAnalyze.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1232/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.15.0  (landing page)
Tal Ashuach
Snapshot Date: 2022-06-29 14:00:05 -0400 (Wed, 29 Jun 2022)
git_url: https://git.bioconductor.org/packages/MPRAnalyze
git_branch: master
git_last_commit: c2fdf6c
git_last_commit_date: 2022-04-26 11:51:23 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MPRAnalyze
Version: 1.15.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MPRAnalyze.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MPRAnalyze_1.15.0.tar.gz
StartedAt: 2022-06-30 03:38:15 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 03:40:50 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 155.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MPRAnalyze.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MPRAnalyze.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MPRAnalyze_1.15.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MPRAnalyze.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MPRAnalyze/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MPRAnalyze' version '1.15.0'
* 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 'MPRAnalyze' 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
getAlpha           6.17   0.03    6.20
analyzeComparative 5.74   0.11    5.85
* 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

MPRAnalyze.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/MPRAnalyze_1.15.0.tar.gz && rm -rf MPRAnalyze.buildbin-libdir && mkdir MPRAnalyze.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MPRAnalyze.buildbin-libdir MPRAnalyze_1.15.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MPRAnalyze_1.15.0.zip && rm MPRAnalyze_1.15.0.tar.gz MPRAnalyze_1.15.0.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
100 50759  100 50759    0     0   885k      0 --:--:-- --:--:-- --:--:--  901k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'MPRAnalyze' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'MPRAnalyze' as MPRAnalyze_1.15.0.zip
* DONE (MPRAnalyze)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'MPRAnalyze' successfully unpacked and MD5 sums checked

Tests output


Example timings

MPRAnalyze.Rcheck/MPRAnalyze-Ex.timings

nameusersystemelapsed
MpraObject0.030.000.03
analyzeComparative5.740.115.85
analyzeQuantification1.890.051.94
estimateDepthFactors0.020.000.02
extractModelParameters0.890.030.92
getAlpha6.170.036.20
getDistrParam1.030.001.03
getFits_DNA1.220.021.24
getFits_RNA101
setDepthFactors0.020.000.01
setModel1.700.011.72
simulateMPRA0.110.000.11
testCoefficient2.940.022.95
testEmpirical1.950.011.97
testLrt3.110.053.16