Back to Multiple platform build/check report for BioC 3.11
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for IgGeneUsage on machv2

This page was generated on 2020-10-17 11:58:43 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IgGeneUsage PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 861/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IgGeneUsage 1.2.2
Simo Kitanovski
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IgGeneUsage
Branch: RELEASE_3_11
Last Commit: 6e5bdb3
Last Changed Date: 2020-07-31 19:10:01 -0400 (Fri, 31 Jul 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  ERROR  skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IgGeneUsage
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IgGeneUsage_1.2.2.tar.gz
StartedAt: 2020-10-17 02:09:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:17:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 487.1 seconds
RetCode: 0
Status:  OK 
CheckDir: IgGeneUsage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IgGeneUsage_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IgGeneUsage.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IgGeneUsage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IgGeneUsage’ version ‘1.2.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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
LOO 226.886  5.669 155.318
DGU  83.960  3.408  76.369
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/IgGeneUsage.Rcheck/00check.log’
for details.



Installation output

IgGeneUsage.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IgGeneUsage
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (IgGeneUsage)

Tests output

IgGeneUsage.Rcheck/tests/testthat.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-apple-darwin17.0 (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
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


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 mod$fit_ptr() : 
  Exception: variable does not exist; processing stage=data initialization; variable name=N_sample; base type=int  (in 'model108ca22ed0754_zibb' at line 24)


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

SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 1: 
Chain 1: Gradient evaluation took 0.000297 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.97 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 2: 
Chain 2Chain 1: : Iteration:    1 / 1500 [  0%]  (Warmup)Gradient evaluation took 0.000303 seconds

Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.03 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 1500 [  0%]  (Warmup)
Chain 2: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 1: Iteration:  250 / 1500 [ 16%]  (Warmup)
Chain 2: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 2: Iteration:  501 / 1500 [ 33%]  (Sampling)
Chain 1: Iteration:  500 / 1500 [ 33%]  (Warmup)
Chain 1: 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: 4.41075 seconds (Warm-up)
Chain 2:                7.63223 seconds (Sampling)
Chain 2:                12.043 seconds (Total)
Chain 2: 
Chain 1: Iteration: 1500 / 1500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 4.9411 seconds (Warm-up)
Chain 1:                8.00058 seconds (Sampling)
Chain 1:                12.9417 seconds (Total)
Chain 1: 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 93 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 42.443   3.014  30.852 

Example timings

IgGeneUsage.Rcheck/IgGeneUsage-Ex.timings

nameusersystemelapsed
DGU83.960 3.40876.369
IGHV_Epitopes0.0030.0020.005
IGHV_HCV0.0040.0020.006
Ig0.0020.0020.004
Ig_SE0.0400.0030.044
LOO226.886 5.669155.318