Package: PathoStat

Version: 1.9.4

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PathoStat_1.9.4.tar.gz

StartedAt: 2019-04-09 02:34:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:39:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 294.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: PathoStat.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PathoStat_1.9.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.9.4’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PathoStat’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘ComplexHeatmap’ ‘RColorBrewer’
  All declared Imports should be used.
* 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 ... ERROR
Running examples in ‘PathoStat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findTaxonomy300
> ### Title: Find the taxonomy for maximum 300 tids
> ### Aliases: findTaxonomy300
> 
> ### ** Examples
> 
> example_data_dir <- system.file("example/data", package = "PathoStat")
> pathoreport_file_suffix <- "-sam-report.tsv"
> datlist <- readPathoscopeData(example_data_dir, 
+ pathoreport_file_suffix, input.files.name.vec = as.character(1:6))
> dat <- datlist$data
> ids <- rownames(dat)
> tids <- unlist(lapply(ids, FUN = grepTid))
> taxonLevels <- findTaxonomy300(tids[1:5])
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Error in the HTTP2 framing layer
Calls: findTaxonomy300 ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PathoStat
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PathoStat’ ...
** 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
* DONE (PathoStat)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(PathoStat)
> 
> test_check("PathoStat")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.836   0.411  12.245 

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	16.772	0.052	16.828
Chisq_Test_Pam	0.006	0.000	0.006
Fisher_Test_Pam	0.007	0.000	0.007
GET_PAM	0.003	0.000	0.003
LOOAUC_simple_multiple_noplot_one_df	4.136	0.000	4.136
LOOAUC_simple_multiple_one_df	4.351	0.004	4.355
PathoStat-class	0.065	0.000	0.066
TranslateIdToTaxLevel	0.003	0.000	0.003
Wilcox_Test_df	0.015	0.000	0.015
findRAfromCount	0.22	0.00	0.22
findTaxonMat	0.368	0.012	1.018
findTaxonomy	0.235	0.008	1.235