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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RNASeqR_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘RNASeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNASeqR’ version ‘1.16.0’
* 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 ‘RNASeqR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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 ... NOTE
AlignmentPlot: no visible binding for global variable ‘value’
Update_Fastq_gz: no visible binding for global variable
  ‘sample.pattern’
Undefined global functions or variables:
  sample.pattern value
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... ERROR
Running examples in ‘RNASeqR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RNASeqRParam-constructor
> ### Title: RNASeqRParam
> ### Aliases: RNASeqRParam-constructor RNASeqRParam
> 
> ### ** Examples
> 
> input_files.path <- system.file("extdata/", package = "RNASeqRData")
> rnaseq_result.path <- tempdir(check = TRUE)
> exp <- RNASeqRParam(path.prefix          = rnaseq_result.path,
+                     input.path.prefix    = input_files.path,
+                     genome.name          = "Saccharomyces_cerevisiae_XV_Ensembl",
+                     sample.pattern       = "SRR[0-9]*_XV",
+                     independent.variable = "state",
+                     case.group           = "60mins_ID20_amphotericin_B",
+                     control.group        = "60mins_ID20_control",
+                     fastq.gz.type        = "PE")
************** Checking input parameters ************

(✔) : Input parameters are all not NA !! 


************** Checking operating system type ************

(✔) : Your system operating system is 'linux'


************** Checking python version ************

(✔) : Python is available on your device!

       ● Python version : 3.8


************** Checking 2to3 command ************

sh: 1: 2to3: not found
Warning in system2("2to3", "--help", stdout = FALSE) :
  error in running command
(✘) : 2to3 command is not available on your device!


************** Setting prefix path ************

(✎) : The following files will be installed under '/tmp/RtmpbweMZH/'


************** Setting input prefix path ************

(✎) : 'input_files' is found under '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/' directory.

       ● Validity of 'input_files/' will be checked.


************** Checking phenodata  ************

▶ Checking whether "raw_fastq.gz files" matches "'ids' of phenodata.csv" 

(✔) : Column 'ids' of phenodata.csv is valid. 

      ● sample ids are : "SRR3396381_XV, SRR3396382_XV, SRR3396384_XV, SRR3396385_XV, SRR3396386_XV, SRR3396387_XV"

(✔) : 'independent.variable' : 'state' is in the column of phenodata.csv. 


▶ Checking whether 'state' is a two-group 'independent.variable' ...

(✔) : Column 'independent.variable' : 'state' of phenodata.csv is valid. 

      ● 'independent.variable' : 'state'


************** Checking hierarchy of '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/input_files/' ************

(✔) : 'Saccharomyces_cerevisiae_XV_Ensembl.gtf' is in 'input_files'

(✔) : 'Saccharomyces_cerevisiae_XV_Ensembl.fa' is in 'input_files'

(✔) : 'raw_fastq.gz/' is in 'input_files'

(✔) : 'raw_fastq.gz/SRR3396381_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396381_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396382_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396382_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396384_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396384_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396385_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396385_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396386_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396386_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396387_XV_1.fastq.gz' is in 'input_files/'

(✔) : 'raw_fastq.gz/SRR3396387_XV_2.fastq.gz' is in 'input_files/'

(✔) : 'phenodata.csv is in 'input_files'

(⚠) : 'indices/' is optional. You can download the corresponding 'XXX.ht2' from 'https://ccb.jhu.edu/software/hisat2/index.shtml' to speed up the process.


(✔) : '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/input_files/' is valid !



************** Checking 'case.group' & 'control.group' ************

(✘) : 'case.group' : '60mins_ID20_amphotericin_B' is not a group of in 'independent.variable'.


Error in CheckCaseControlGroup(input.path.prefix, independent.variable,  : 
  'case.group' invalid ERROR
Calls: RNASeqRParam -> CheckCaseControlGroup
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RNASeqR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RNASeqR
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘RNASeqR’ ...
** 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
Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor
  version 3.17
** testing if installed package can be loaded from final location
Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor
  version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (RNASeqR)