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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings netDx_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netDx.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.11.0’
* 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:
  .BBSoptions
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 ‘netDx’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'netDx' was found
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 loading without being on the library search path ... WARNING
Error in library(netDx, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘netDx’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.           \-ExperimentHub (local) .local(x, i, j = j, ...)
   10.             +-methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
   11.             | \-base::eval(call, callEnv)
   12.             |   \-base::eval(call, callEnv)
   13.             \-AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
   14.               \-AnnotationHub (local) .local(x, i, j = j, ...)
   15.                 \-AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
   16.                   \-base::tryCatch(...)
   17.                     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   18.                       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   19.                         \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RawDataConversion.Rmd’ using ‘UTF-8’... OK
  ‘ThreeWayClassifier.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ...

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netDx
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘netDx’ ...
** 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 (netDx)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(netDx)

Attaching package: 'netDx'

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

    predict

> 
> test_check("netDx")
         TT_STATUS
STATUS    TEST TRAIN
  LumA      52   178
  notLumA   52   243
         PRED_CLASS
STATUS    LumA notLumA
  LumA      41      11
  notLumA   17      35
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 29 ]

== Failed tests ================================================================
-- Error ('test_psn_construction.R:16'): (code run outside of `test_that()`) ---
Error: failed to load resource
  name: EH598
  title: BRCA_RPPAArray-20160128
  reason: 1 resources failed to download
Backtrace:
     x
  1. +-base::suppressMessages(...) at test_psn_construction.R:16:4
  2. | \-base::withCallingHandlers(...)
  3. \-curatedTCGAData::curatedTCGAData(...)
  4.   \-curatedTCGAData:::.getResources(...)
  5.     \-base::lapply(...)
  6.       \-curatedTCGAData (local) FUN(X[[i]], ...)
  7.         +-query(ExperimentHub, res)[[1L]]
  8.         \-query(ExperimentHub, res)[[1L]]
  9.           \-ExperimentHub (local) .local(x, i, j = j, ...)
 10.             +-methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
 11.             | \-base::eval(call, callEnv)
 12.             |   \-base::eval(call, callEnv)
 13.             \-AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
 14.               \-AnnotationHub (local) .local(x, i, j = j, ...)
 15.                 \-AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
 16.                   \-base::tryCatch(...)
 17.                     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.                       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19.                         \-value[[3L]](cond)

[ FAIL 1 | WARN 5 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted