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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings bioCancer_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/bioCancer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.28.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    app       3.3Mb
    extdata   1.6Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    metamorphosis: bioCancer is a radiant.data extension
  Cannot process chunk/lines:
    reduce size of package by half 14 -> 7 mb
  Cannot process chunk/lines:
    improve Reactome_ui functions
  Cannot process chunk/lines:
    add switch button to ui_circomics
  Cannot process chunk/lines:
    improve circomics functions
  Cannot process chunk/lines:
    delete commented files and figures
  Cannot process chunk/lines:
    cleanup ui_radiant, /Rbis, /quant, /bioCancer
  Cannot process chunk/lines:
    switchButton
  Cannot process chunk/lines:
    data.row.names(row.names, rowsi, i) :
  Cannot process chunk/lines:
    some row.names duplicated: 11,12,13,14 --> row.names NOT used
  Cannot process chunk/lines:
    dplyr::mutate_each() is deprecated
  Cannot process chunk/lines:
    dply::summarise_each() is deprecated
  Cannot process chunk/lines:
    replace BiocStyle by prettydoc
  Cannot process chunk/lines:
    Warning in formals(fun) : argument is not a function
  Cannot process chunk/lines:
    Warning in body(fun) : argument is not a function
  Cannot process chunk/lines:
    Fix setting plot size
  Cannot process chunk/lines:
    Change the color rang of Circular layout plot as in standards
  Cannot process chunk/lines:
    update Correlation Methods
  Cannot process chunk/lines:
    replace .libPath() by path.package('bioCancer') in portal.R file
* 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 ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘GO.db’ ‘R.methodsS3’ ‘import’ ‘methods’ ‘org.Bt.eg.db’
  ‘shinythemes’
  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 ... NOTE
getGenesClassification: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'getCancerStudies.CGDS':
  ‘getCancerStudies.CGDS’

S3 methods shown with full name in documentation object 'getCaseLists.CGDS':
  ‘getCaseLists.CGDS’

S3 methods shown with full name in documentation object 'getClinicalData.CGDS':
  ‘getClinicalData.CGDS’

S3 methods shown with full name in documentation object 'getGeneticProfiles.CGDS':
  ‘getGeneticProfiles.CGDS’

S3 methods shown with full name in documentation object 'getMutationData.CGDS':
  ‘getMutationData.CGDS’

S3 methods shown with full name in documentation object 'getProfileData.CGDS':
  ‘getProfileData.CGDS’

S3 methods shown with full name in documentation object 'processURL.CGDS':
  ‘processURL.CGDS’

S3 methods shown with full name in documentation object 'setVerbose.CGDS':
  ‘setVerbose.CGDS’

S3 methods shown with full name in documentation object 'test.CGDS':
  ‘test.CGDS’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘bioCancer.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/bioCancer.Rcheck/00check.log’
for details.

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

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

Loading required package: ggplot2
Loading required package: lubridate

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Loading required package: tidyr

Attaching package: 'tidyr'

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

    extract

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

    matches

Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'radiant.data'

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

    month, wday

The following object is masked from 'package:ggplot2':

    diamonds

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

    set_attr

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

    describe

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

    date

Loading required package: XML


> 
> test_check("bioCancer")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
ReactomeFI connection...  OK
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_funs.R:8:1', 'test_funs.R:14:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  9.284   0.553  10.414