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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.7.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AlpsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlpsNMR' version '4.7.1'
* 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 whether package 'AlpsNMR' 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'AlpsNMR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Peak_detection
> ### Title: Peak detection for NMR
> ### Aliases: Peak_detection
> 
> ### ** Examples
> 
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> nmr_dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
> # Low resolution:
> dataset_1D <- nmr_interpolate_1D(nmr_dataset, axis = c(min = -0.5, max = 10, by = 0.001))
> dataset_1D <- nmr_exclude_region(dataset_1D, exclude = list(water = c(4.7, 5)))
> 
> # 1. Optimize peak detection parameters:
> range_without_peaks <- c(9.5, 10)
> # Choose a region without peaks:
> plot(dataset_1D, chemshift_range = range_without_peaks)
> baselineThresh <- nmr_baseline_threshold(dataset_1D, range_without_peaks = range_without_peaks)
> # Plot to check the baseline estimations
> nmr_baseline_threshold_plot(
+     dataset_1D,
+     baselineThresh,
+     NMRExperiment = "all",
+     chemshift_range = range_without_peaks
+ )
> 
> # 1.Peak detection in the dataset.
> peak_data <- nmr_detect_peaks(
+     dataset_1D,
+     nDivRange_ppm = 0.1, # Size of detection segments
+     scales = seq(1, 16, 2),
+     baselineThresh = NULL, # Minimum peak intensity
+     SNR.Th = 4, # Signal to noise ratio
+     range_without_peaks = range_without_peaks, # To estimate
+ )
> 
> sample_10 <- filter(dataset_1D, NMRExperiment == "10")
> # nmr_detect_peaks_plot(sample_10, peak_data, "NMRExp_ref")
> 
> peaks_detected <- nmr_detect_peaks_tune_snr(
+     sample_10,
+     SNR_thresholds = seq(from = 2, to = 3, by = 0.5),
+     nDivRange_ppm = 0.03,
+     scales = seq(1, 16, 2),
+     baselineThresh = 0
+ )
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE,  :
  port 11515 cannot be opened

Error: BiocParallel errors
  1 remote errors, element index: 3
  0 unevaluated and other errors
  first remote error:
Error in socketConnection(port = port, server = TRUE, blocking = TRUE, : cannot open the connection
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 ... 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
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'AlpsNMR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (AlpsNMR)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(AlpsNMR)

Attaching package: 'AlpsNMR'

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

    filter

> 
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
  20.96    1.34   68.09