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CHECK report for IgGeneUsage on tokay1

This page was generated on 2020-04-15 12:32:55 -0400 (Wed, 15 Apr 2020).

Package 830/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IgGeneUsage 1.0.1
Simo Kitanovski
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/IgGeneUsage
Branch: RELEASE_3_10
Last Commit: ca78a4e
Last Changed Date: 2020-04-04 07:00:49 -0400 (Sat, 04 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IgGeneUsage
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IgGeneUsage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings IgGeneUsage_1.0.1.tar.gz
StartedAt: 2020-04-15 04:00:51 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:22:29 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1297.3 seconds
RetCode: 0
Status:  OK  
CheckDir: IgGeneUsage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IgGeneUsage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings IgGeneUsage_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/IgGeneUsage.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IgGeneUsage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IgGeneUsage' 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 'IgGeneUsage' 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 or elapsed time > 5s
     user system elapsed
LOO 10.88   1.77  269.74
DGU  4.33   0.20   89.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
LOO 8.80   1.63  222.05
DGU 6.53   0.27  120.37
* 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

IgGeneUsage.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/IgGeneUsage_1.0.1.tar.gz && rm -rf IgGeneUsage.buildbin-libdir && mkdir IgGeneUsage.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IgGeneUsage.buildbin-libdir IgGeneUsage_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL IgGeneUsage_1.0.1.zip && rm IgGeneUsage_1.0.1.tar.gz IgGeneUsage_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 46717  100 46717    0     0   521k      0 --:--:-- --:--:-- --:--:--  543k

install for i386

* installing *source* package 'IgGeneUsage' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IgGeneUsage'
    finding HTML links ... done
    DGU                                     html  
    IGHV_Epitopes                           html  
    IGHV_HCV                                html  
    Ig                                      html  
    Ig_SE                                   html  
    LOO                                     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 'IgGeneUsage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IgGeneUsage' as IgGeneUsage_1.0.1.zip
* DONE (IgGeneUsage)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'IgGeneUsage' successfully unpacked and MD5 sums checked

Tests output

IgGeneUsage.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> library(testthat)
> library(IgGeneUsage)
Loading required package: Rcpp
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Loading required package: StanHeaders
> 
> test_check("IgGeneUsage")
Error in t.test.formula((Ys[x, ]/Ns) ~ Xs) : 
  grouping factor must have exactly 2 levels
Error in t.test.default(x = 0, y = 0) : not enough 'x' observations
Error in t.test.default(x = 0, y = c(0, 0)) : not enough 'x' observations
Error in wilcox.test.formula((Ys[x, ]/Ns) ~ Xs) : 
  grouping factor must have exactly 2 levels
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : 
  Exception: variable does not exist; processing stage=data initialization; variable name=N_sample; base type=int  (in 'model31c82f4235b9_zibb' at line 24)

starting worker pid=6008 on localhost:11466 at 04:18:20.851
starting worker pid=12416 on localhost:11466 at 04:18:21.407

SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).

SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0.001 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 10 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 1: 
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 2: Iteration:    1 / 1500 [  0%]  (Warmup)
Chain 1: Iteration:    1 / 1500 [  0%]  (Warmup)
Chain 1: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 2: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 1: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 2: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 1: Iteration:  501 / 1500 [ 33%]  (Sampling)
Chain 2: Iteration:  501 / 1500 [ 33%]  (Sampling)
Chain 2: Iteration:  750 / 1500 [ 50%]  (Sampling)
Chain 1: Iteration:  750 / 1500 [ 50%]  (Sampling)
Chain 2: Iteration: 1000 / 1500 [ 66%]  (Sampling)
Chain 1: Iteration: 1000 / 1500 [ 66%]  (Sampling)
Chain 2: Iteration: 1250 / 1500 [ 83%]  (Sampling)
Chain 1: Iteration: 1250 / 1500 [ 83%]  (Sampling)
Chain 2: Iteration: 1500 / 1500 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 7.06 seconds (Warm-up)
Chain 2:                11.067 seconds (Sampling)
Chain 2:                18.127 seconds (Total)
Chain 2: 
Chain 1: Iteration: 1500 / 1500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 7.055 seconds (Warm-up)
Chain 1:                11.922 seconds (Sampling)
Chain 1:                18.977 seconds (Total)
Chain 1: 
== testthat results  ===========================================================
[ OK: 93 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.81    0.93  183.31

IgGeneUsage.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> library(testthat)
> library(IgGeneUsage)
Loading required package: Rcpp
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Loading required package: StanHeaders
> 
> test_check("IgGeneUsage")
Error in t.test.formula((Ys[x, ]/Ns) ~ Xs) : 
  grouping factor must have exactly 2 levels
Error in t.test.default(x = 0, y = 0) : not enough 'x' observations
Error in t.test.default(x = 0, y = c(0, 0)) : not enough 'x' observations
Error in wilcox.test.formula((Ys[x, ]/Ns) ~ Xs) : 
  grouping factor must have exactly 2 levels
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : 
  Exception: variable does not exist; processing stage=data initialization; variable name=N_sample; base type=int  (in 'model2c8c6b883f7b_zibb' at line 24)

starting worker pid=11296 on localhost:11861 at 04:21:59.491
starting worker pid=12748 on localhost:11861 at 04:21:59.915

SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 1500 [  0%]  (Warmup)

SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 1500 [  0%]  (Warmup)
Chain 1: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 2: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 1: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 1: Iteration:  501 / 1500 [ 33%]  (Sampling)
Chain 2: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 2: Iteration:  501 / 1500 [ 33%]  (Sampling)
Chain 1: Iteration:  750 / 1500 [ 50%]  (Sampling)
Chain 2: Iteration:  750 / 1500 [ 50%]  (Sampling)
Chain 1: Iteration: 1000 / 1500 [ 66%]  (Sampling)
Chain 2: Iteration: 1000 / 1500 [ 66%]  (Sampling)
Chain 1: Iteration: 1250 / 1500 [ 83%]  (Sampling)
Chain 2: Iteration: 1250 / 1500 [ 83%]  (Sampling)
Chain 1: Iteration: 1500 / 1500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 4.591 seconds (Warm-up)
Chain 1:                7.605 seconds (Sampling)
Chain 1:                12.196 seconds (Total)
Chain 1: 
Chain 2: Iteration: 1500 / 1500 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 5.846 seconds (Warm-up)
Chain 2:                8.383 seconds (Sampling)
Chain 2:                14.229 seconds (Total)
Chain 2: 
== testthat results  ===========================================================
[ OK: 93 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.21    0.76  214.25

Example timings

IgGeneUsage.Rcheck/examples_i386/IgGeneUsage-Ex.timings

nameusersystemelapsed
DGU 4.33 0.2089.61
IGHV_Epitopes0.020.000.02
IGHV_HCV0.020.000.02
Ig000
Ig_SE0.010.020.03
LOO 10.88 1.77269.74

IgGeneUsage.Rcheck/examples_x64/IgGeneUsage-Ex.timings

nameusersystemelapsed
DGU 6.53 0.27120.37
IGHV_Epitopes000
IGHV_HCV0.010.000.01
Ig000
Ig_SE0.050.000.05
LOO 8.80 1.63222.05