##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.30.0’
* 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:
  .devcontainer
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 ‘psichomics’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'createSparklines.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'renderGeneticInfo.Rd':
  ‘ns’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘psichomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getTCGAdataTypes
> ### Title: Get available parameters for TCGA data
> ### Aliases: getTCGAdataTypes getFirebrowseDataTypes getTCGAdates
> ###   getFirebrowseDates getTCGAcohorts getFirebrowseCohorts
> 
> ### ** Examples
> 
> getTCGAdataTypes()
$`RNA sequencing`
  Junction quantification       Exon quantification           Exon expression 
"junction_quantification"     "exon_quantification"         "exon_expression" 
      Junction expression                RSEM genes     RSEM genes normalized 
    "junction_expression"              "RSEM_genes"   "RSEM_genes_normalized" 
            RSEM isoforms                Preprocess 
          "RSEM_isoforms"              "Preprocess" 

> if (isFirebrowseUp()) getTCGAdates()
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                                         <!DOCTYPE html PUBLIC "-//W3C//
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─psichomics::getFirebrowseCohorts() at testFirebrowse.R:87:5
   2.   └─psichomics:::parseFirebrowseMetadata("Cohorts", cohort = cohort)
   3.     └─jsonlite::fromJSON(content(response, "text", encoding = "UTF8"))
   4.       └─jsonlite:::parse_and_simplify(...)
   5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   6.           └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 4 | WARN 0 | SKIP 5 | PASS 1392 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c progressBar.cpp -o progressBar.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-psichomics/00new/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (psichomics)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.188   0.078   0.480 

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.30.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
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Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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Retrieving SUPPA annotation...

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

EXSK

IR

MERGE3m

MIC

MULTI
[ FAIL 4 | WARN 0 | SKIP 5 | PASS 1392 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• Could not resolve host name (1): 'testFirebrowse.R:110:9'
• Couldn't resolve host name (1): 'testGeneInfo.R:99:5'
• On Bioconductor (2): 'testDiscardLowCoveragePSIs.R:62:5',
  'testGeneInfo.R:50:5'
• On CRAN (1): 'testSRAloading.R:4:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testFirebrowse.R:31:5'): queryFirebrowseData queries the Firebrowse web API ──
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

Backtrace:
    ▆
 1. └─psichomics:::queryFirebrowseData(cohort = cohort) at testFirebrowse.R:31:5
 2.   └─psichomics::getTCGAdates()
 3.     └─psichomics:::parseFirebrowseMetadata("Dates")
 4.       └─jsonlite::fromJSON(content(response, "text", encoding = "UTF8"))
 5.         └─jsonlite:::parse_and_simplify(...)
 6.           └─jsonlite:::parseJSON(txt, bigint_as_char)
 7.             └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('testFirebrowse.R:55:5'): parseFirebrowseMetadata parses metadata from Firebrowse ──
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

Backtrace:
    ▆
 1. └─psichomics:::parseFirebrowseMetadata("Cohorts") at testFirebrowse.R:55:5
 2.   └─jsonlite::fromJSON(content(response, "text", encoding = "UTF8"))
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('testFirebrowse.R:78:5'): getFirebrowseDates obtains the datestamps of the data available ──
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

Backtrace:
    ▆
 1. └─psichomics::getFirebrowseDates() at testFirebrowse.R:78:5
 2.   └─psichomics:::parseFirebrowseMetadata("Dates")
 3.     └─jsonlite::fromJSON(content(response, "text", encoding = "UTF8"))
 4.       └─jsonlite:::parse_and_simplify(...)
 5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
 6.           └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('testFirebrowse.R:87:5'): getFirebrowseCohorts obtains the cohorts available ──
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

Backtrace:
    ▆
 1. └─psichomics::getFirebrowseCohorts() at testFirebrowse.R:87:5
 2.   └─psichomics:::parseFirebrowseMetadata("Cohorts", cohort = cohort)
 3.     └─jsonlite::fromJSON(content(response, "text", encoding = "UTF8"))
 4.       └─jsonlite:::parse_and_simplify(...)
 5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
 6.           └─jsonlite:::parse_string(txt, bigint_as_char)

[ FAIL 4 | WARN 0 | SKIP 5 | PASS 1392 ]
Error: Test failures
Execution halted