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CHECK report for NPARC on tokay2

This page was generated on 2020-10-17 11:57:17 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE NPARC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1204/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NPARC 1.0.1
Nils Kurzawa
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/NPARC
Branch: RELEASE_3_11
Last Commit: 6f58e00
Last Changed Date: 2020-05-04 12:12:55 -0400 (Mon, 04 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NPARC
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NPARC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NPARC_1.0.1.tar.gz
StartedAt: 2020-10-17 06:31:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:32:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 89.5 seconds
RetCode: 0
Status:  OK  
CheckDir: NPARC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NPARC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NPARC_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/NPARC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NPARC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NPARC' version '1.0.1'
* 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 'NPARC' 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
getParams 6.47   0.07    6.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
getParams 7.33    0.1    7.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'init_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'init_tests.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

NPARC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/NPARC_1.0.1.tar.gz && rm -rf NPARC.buildbin-libdir && mkdir NPARC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NPARC.buildbin-libdir NPARC_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL NPARC_1.0.1.zip && rm NPARC_1.0.1.tar.gz NPARC_1.0.1.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 1622k  100 1622k    0     0  21.0M      0 --:--:-- --:--:-- --:--:-- 22.9M

install for i386

* installing *source* package 'NPARC' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NPARC'
    finding HTML links ... done
    NPARCtest                               html  
    fitSingleSigmoid                        html  
    getParams                               html  
    nparc                                   html  
    nparcFit                                html  
    runNPARC                                html  
    stauro_TPP_data_tidy                    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 'NPARC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NPARC' as NPARC_1.0.1.zip
* DONE (NPARC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'NPARC' successfully unpacked and MD5 sums checked

Tests output

NPARC.Rcheck/tests_i386/init_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> data(stauro_TPP_data_tidy)
Warning message:
In data(stauro_TPP_data_tidy) : data set 'stauro_TPP_data_tidy' not found
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(magrittr)
> library(NPARC)
> library(testthat)

Attaching package: 'testthat'

The following objects are masked from 'package:magrittr':

    equals, is_less_than, not

The following object is masked from 'package:dplyr':

    matches

> 
> ATP_targets_stauro <- filter(stauro_TPP_data_tidy, grepl("ATP|STK4_", uniqueID))
> atp_ids <- ATP_targets_stauro$uniqueID
> rss0_ref <- c( 0.042328688, 0.574210782, 1.105606894, 66.141814549, 1.279980245, 1.445979905, NA, 0.085035397, NA, 0.086908456, 0.040746912, 0.229219646, 0.185040763, 0.069901302, 3.219166488, 0.890621716, 1.482869417, 0.111385691, 0.890474276, 0.096161260, 0.005317976, 0.165361410, 0.261380998, 2.004720774, NA, 1.017639038, 0.037805608, 0.079748130, 0.080865091, 0.023917017, 0.302070404, 0.438928745, 0.021234921, 0.207783991, 0.511561035, NA, 0.047061699, 0.022204837, 0.018557014, 82.669418181, 0.171696257, 0.246755638, 0.027504901, 0.042566445, 0.685432518, 1.2181315672231198821)
> rss1_ref <- c( NA, 0.52452012, 1.02728630, NA, 1.16253040, NA, NA, NA, NA, 0.08085710, 0.03391284, 0.19178616, 0.11715310, 0.05738689, 2.85347619, NA, 0.88566800, NA, 0.86233078, 0.05913776, NA, NA, 0.24112396, NA, NA, NA, 0.03726856, 0.07672426, 0.07933303, 0.02046256, NA, 0.42376129, 0.01929703, 0.19330061, 0.49355960, NA, 0.03926680, 0.01932926, NA, 82.39894648, 0.14698662, 0.22814391, 0.02189395, 0.03691358, 0.57373856, 0.083147452021042442)
> rssDiff_ref <- c(NA, 0.0496906604, 0.0783205890, NA, 0.1174498426, NA, NA, NA, NA, 0.0060513570, 0.0068340678, 0.0374334892, 0.0678876612, 0.0125144109, 0.3656902966, NA, 0.5972014163, NA, 0.0281434961, 0.0370234978, NA, NA, 0.0202570335, NA, NA, NA, 0.0005370464, 0.0030238719, 0.0015320641, 0.0034544609, NA, 0.0151674541, 0.0019378859, 0.0144833862, 0.0180014361, NA, 0.0077948980, 0.0028755747, NA, 0.2704717055, 0.0247096421, 0.0186117273, 0.0056109477, 0.0056528626, 0.1116939612, 1.13498411520207742598)
> n0_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> n1_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> repeats_ref <- c(11, 0, 0, 11, 0, 11, 11, 11, 11, 0, 0, 0, 0, 0, 0, 11, 0, 11, 0, 0, 11, 11, 0, 11, 11, 11, 0, 0, 0, 0, 11, 0, 0, 0, 0, 11, 0, 0, 11, 0, 0, 0, 0, 0, 0, 0)
> tm_0_ref <- c(NA, 61.733018503993208, NaN, NA, NaN, NaN, NA, NA, NA, 45.507090381927227, 48.370656179268586, 46.177862386428778, NaN, 50.747974622093842, 51.108100718477552, NA, 53.716668890572350, NA, 49.944382649054042, 53.268268043773986, NA, 64.083619744519751, 52.630782071773126, 54.403632566800773, NA, NA, 49.973318102061327, 54.987190448048963, 55.650774547079479, 53.776217585739715, NA, 63.931766238670086, 53.474065831051554, 59.660513721432004, 53.651458551339147, NA, 53.400317830126923, 56.166341210006678, NA, 49.957133804531374, 58.379308939431617, 61.739135919243360, 49.739613672120782, 51.424194381078600, NaN, 51.075584610286953)
> tm_20_ref <- c(51.826211134785211, 66.548397028205514, 77.195149424582979, 55.304171825879109, 54.826147979730159, NA, NA, 56.362667583506500, NA, 45.626792065465864, 48.448244898573385, 47.460807063834899, 60.921156578436033, 50.709466817179830, NaN,                NaN,                NaN, 53.705720351822045, 50.199251315345073, 51.808623346193485, 54.052321351744041, NA, 51.186531862923864, NA, NA,                NaN, 50.030558335114812, 54.702758421926561, 55.813688161147894, 53.533856781624372, 49.760889873698368, 63.528237092905130, 53.782382421569636, 60.003138034648828, 53.162997375385423, NA, 53.292278053288818, 56.235749170195618, 53.673086380853192, 55.280037025265500, 59.676701562973001, 60.694252715919731, 49.732243787451694, 51.158615360263845, 70.641541915911802, 59.740907732406420)
> pAdj_ref <- c(NA, 0.699795397624508708, 0.753523752550566694, NA, 0.861339846144721699, NA, NA, NA, NA, 0.753523752550566694, 0.315762492309564990, 0.315762492309564990, 0.019064553849503785, 0.315762492309564990, 0.861339846144721699, NA, 0.315762492309564990, NA, 0.861339846144721699, 0.077448008418172787, NA, NA, 0.861339846144721699, NA, NA, NA, 0.983055252694920556, 0.861339846144721699, 0.945666731555014795, 0.368321920466761210, NA, 0.861339846144721699, 0.695132899776564450, 0.861339846144721699, 0.861339846144721699, NA, 0.315762492309564990, 0.695132899776564450, NA, 0.997288089402401878, 0.368321920466761210, 0.753523752550566694, 0.315762492309564990, 0.411224424237822794, 0.315762492309564990, 0.000000000000000000)
> 
> 
> proc.time()
   user  system elapsed 
   1.15    0.15    1.28

NPARC.Rcheck/tests_x64/init_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> data(stauro_TPP_data_tidy)
Warning message:
In data(stauro_TPP_data_tidy) : data set 'stauro_TPP_data_tidy' not found
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(magrittr)
> library(NPARC)
> library(testthat)

Attaching package: 'testthat'

The following objects are masked from 'package:magrittr':

    equals, is_less_than, not

The following object is masked from 'package:dplyr':

    matches

> 
> ATP_targets_stauro <- filter(stauro_TPP_data_tidy, grepl("ATP|STK4_", uniqueID))
> atp_ids <- ATP_targets_stauro$uniqueID
> rss0_ref <- c( 0.042328688, 0.574210782, 1.105606894, 66.141814549, 1.279980245, 1.445979905, NA, 0.085035397, NA, 0.086908456, 0.040746912, 0.229219646, 0.185040763, 0.069901302, 3.219166488, 0.890621716, 1.482869417, 0.111385691, 0.890474276, 0.096161260, 0.005317976, 0.165361410, 0.261380998, 2.004720774, NA, 1.017639038, 0.037805608, 0.079748130, 0.080865091, 0.023917017, 0.302070404, 0.438928745, 0.021234921, 0.207783991, 0.511561035, NA, 0.047061699, 0.022204837, 0.018557014, 82.669418181, 0.171696257, 0.246755638, 0.027504901, 0.042566445, 0.685432518, 1.2181315672231198821)
> rss1_ref <- c( NA, 0.52452012, 1.02728630, NA, 1.16253040, NA, NA, NA, NA, 0.08085710, 0.03391284, 0.19178616, 0.11715310, 0.05738689, 2.85347619, NA, 0.88566800, NA, 0.86233078, 0.05913776, NA, NA, 0.24112396, NA, NA, NA, 0.03726856, 0.07672426, 0.07933303, 0.02046256, NA, 0.42376129, 0.01929703, 0.19330061, 0.49355960, NA, 0.03926680, 0.01932926, NA, 82.39894648, 0.14698662, 0.22814391, 0.02189395, 0.03691358, 0.57373856, 0.083147452021042442)
> rssDiff_ref <- c(NA, 0.0496906604, 0.0783205890, NA, 0.1174498426, NA, NA, NA, NA, 0.0060513570, 0.0068340678, 0.0374334892, 0.0678876612, 0.0125144109, 0.3656902966, NA, 0.5972014163, NA, 0.0281434961, 0.0370234978, NA, NA, 0.0202570335, NA, NA, NA, 0.0005370464, 0.0030238719, 0.0015320641, 0.0034544609, NA, 0.0151674541, 0.0019378859, 0.0144833862, 0.0180014361, NA, 0.0077948980, 0.0028755747, NA, 0.2704717055, 0.0247096421, 0.0186117273, 0.0056109477, 0.0056528626, 0.1116939612, 1.13498411520207742598)
> n0_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> n1_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> repeats_ref <- c(11, 0, 0, 11, 0, 11, 11, 11, 11, 0, 0, 0, 0, 0, 0, 11, 0, 11, 0, 0, 11, 11, 0, 11, 11, 11, 0, 0, 0, 0, 11, 0, 0, 0, 0, 11, 0, 0, 11, 0, 0, 0, 0, 0, 0, 0)
> tm_0_ref <- c(NA, 61.733018503993208, NaN, NA, NaN, NaN, NA, NA, NA, 45.507090381927227, 48.370656179268586, 46.177862386428778, NaN, 50.747974622093842, 51.108100718477552, NA, 53.716668890572350, NA, 49.944382649054042, 53.268268043773986, NA, 64.083619744519751, 52.630782071773126, 54.403632566800773, NA, NA, 49.973318102061327, 54.987190448048963, 55.650774547079479, 53.776217585739715, NA, 63.931766238670086, 53.474065831051554, 59.660513721432004, 53.651458551339147, NA, 53.400317830126923, 56.166341210006678, NA, 49.957133804531374, 58.379308939431617, 61.739135919243360, 49.739613672120782, 51.424194381078600, NaN, 51.075584610286953)
> tm_20_ref <- c(51.826211134785211, 66.548397028205514, 77.195149424582979, 55.304171825879109, 54.826147979730159, NA, NA, 56.362667583506500, NA, 45.626792065465864, 48.448244898573385, 47.460807063834899, 60.921156578436033, 50.709466817179830, NaN,                NaN,                NaN, 53.705720351822045, 50.199251315345073, 51.808623346193485, 54.052321351744041, NA, 51.186531862923864, NA, NA,                NaN, 50.030558335114812, 54.702758421926561, 55.813688161147894, 53.533856781624372, 49.760889873698368, 63.528237092905130, 53.782382421569636, 60.003138034648828, 53.162997375385423, NA, 53.292278053288818, 56.235749170195618, 53.673086380853192, 55.280037025265500, 59.676701562973001, 60.694252715919731, 49.732243787451694, 51.158615360263845, 70.641541915911802, 59.740907732406420)
> pAdj_ref <- c(NA, 0.699795397624508708, 0.753523752550566694, NA, 0.861339846144721699, NA, NA, NA, NA, 0.753523752550566694, 0.315762492309564990, 0.315762492309564990, 0.019064553849503785, 0.315762492309564990, 0.861339846144721699, NA, 0.315762492309564990, NA, 0.861339846144721699, 0.077448008418172787, NA, NA, 0.861339846144721699, NA, NA, NA, 0.983055252694920556, 0.861339846144721699, 0.945666731555014795, 0.368321920466761210, NA, 0.861339846144721699, 0.695132899776564450, 0.861339846144721699, 0.861339846144721699, NA, 0.315762492309564990, 0.695132899776564450, NA, 0.997288089402401878, 0.368321920466761210, 0.753523752550566694, 0.315762492309564990, 0.411224424237822794, 0.315762492309564990, 0.000000000000000000)
> 
> 
> proc.time()
   user  system elapsed 
   1.48    0.07    1.54

Example timings

NPARC.Rcheck/examples_i386/NPARC-Ex.timings

nameusersystemelapsed
NPARCtest2.650.132.78
fitSingleSigmoid0.290.040.33
getParams6.470.076.54
nparcFit2.560.012.57
runNPARC2.530.032.57

NPARC.Rcheck/examples_x64/NPARC-Ex.timings

nameusersystemelapsed
NPARCtest3.070.073.15
fitSingleSigmoid0.290.050.33
getParams7.330.107.42
nparcFit2.730.032.76
runNPARC2.630.042.68