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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 861/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IgGeneUsage 1.2.2 Simo Kitanovski
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
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### Running command:
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### /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
###
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* 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.
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)
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
IgGeneUsage.Rcheck/IgGeneUsage-Ex.timings
| name | user | system | elapsed | |
| DGU | 83.960 | 3.408 | 76.369 | |
| IGHV_Epitopes | 0.003 | 0.002 | 0.005 | |
| IGHV_HCV | 0.004 | 0.002 | 0.006 | |
| Ig | 0.002 | 0.002 | 0.004 | |
| Ig_SE | 0.040 | 0.003 | 0.044 | |
| LOO | 226.886 | 5.669 | 155.318 | |