##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rawrr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rawrr_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rawrr.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rawrr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawrr’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
 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 ‘rawrr’ 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 loading without being on the library search path ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rawrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readChromatogram
> ### Title: Extracts chromatographic data from a raw file.
> ### Aliases: readChromatogram
> 
> ### ** Examples
> 
> 
> # Example 1: not meaningful but proof-of-concept
> (rawfile <- rawrr::sampleFilePath())
[1] "/home/biocbuild/bbs-3.22-bioc/R/site-library/rawrr/extdata/sample.raw"
> 
> rawrr::readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000) |>
+     plot()
> rawrr::readChromatogram(rawfile, type='bpc') |> plot()
> rawrr::readChromatogram(rawfile, type='tic') |> plot()
> 
> # Example 2: extract iRT peptides
>  if (require(ExperimentHub) & require(protViz)){
+ iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
+   "GAGSSEPVTGLDAK", "TPVISGGPYEYR", "VEATFGVDESNAK",
+   "TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK",
+   "LFLQFGAQGSPFLK")
+ 
+ 
+ # fetch via ExperimentHub
+ library(ExperimentHub)
+ eh <- ExperimentHub::ExperimentHub()
+ EH4547 <- normalizePath(eh[["EH4547"]])
+ 
+ (rawfile <- paste0(EH4547, ".raw"))
+ if (!file.exists(rawfile)){
+     file.link(EH4547, rawfile)
+ }
+ op <- par(mfrow=c(2,1))
+ readChromatogram(rawfile, type='bpc') |> plot()
+ readChromatogram(rawfile, type='tic') |> plot()
+ par(op)
+ 
+ # derive [2H+] ions
+ ((protViz::parentIonMass(iRTpeptide) + 1.008) / 2) |>
+    readChromatogram(rawfile=rawfile) |>
+    plot()
+ }
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: protViz
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:
  SSL connection timeout
    Consider rerunning with 'localHub=TRUE'
  Backtrace:
      ▆
   1. └─ExperimentHub::ExperimentHub() at test-EH4547.R:12:5
   2.   └─AnnotationHub::.Hub(...)
   3.     └─base::tryCatch(...)
   4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 94 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘rawrr.Rmd’ using rmarkdown

Quitting from rawrr.Rmd:106-116 [tartareEH4547]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub()
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rawrr.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘rawrr.Rmd’

SUMMARY: processing the following file failed:
  ‘rawrr.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/rawrr.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rawrr
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘rawrr’ ...
** this is package ‘rawrr’ version ‘1.18.0’
** using staged installation
** R
** 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 (rawrr)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(rawrr))
> 
> if (rawrr:::.getRawrrAssemblyVersion() < "1.17.2"){
+   rawrr::installRawrrExe(force = TRUE)
+ }
> 
> test_check("rawrr")
Saving _problems/test-EH4547-12.R
Total Ion Current:	 78725448
Scan Low Mass:	 350
Scan High Mass:	 1800
Scan Start Time (min):	 0.001619751
Scan Number:	 1
Base Peak Intensity:	 5979308
Base Peak Mass:	 445.1181
Scan Mode:	 FTMS + c NSI Full ms [350.0000-1800.0000]
======= Instrument data =====   :	NULL
Multiple Injection:	ii
Multi Inject Info:	IT=28;28 
AGC:	On
Micro Scan Count:	1
Scan Segment:	1
Scan Event:	1
Master Index:	0
Charge State:	0
Monoisotopic M/Z:	0.0000
Ion Injection Time (ms):	55.000
Max. Ion Time (ms):	55.00
FT Resolution:	120000
MS2 Isolation Width:	1450.00
MS2 Isolation Offset:	0.00
AGC Target:	3000000
HCD Energy:	
Analyzer Temperature:	27.06
=== Mass Calibration:	NULL
Conversion Parameter B:	211820589.2896
Conversion Parameter C:	-41163067.8349
Temperature Comp. (ppm):	-2.35
RF Comp. (ppm):	-0.09
Space Charge Comp. (ppm):	-2.30
Resolution Comp. (ppm):	0.57
Number of Lock Masses:	0
Lock Mass #1 (m/z):	0.0000
Lock Mass #2 (m/z):	0.0000
Lock Mass #3 (m/z):	0.0000
LM Search Window (ppm):	0.0
LM Search Window (mmu):	0.0
Number of LM Found:	0
Last Locking (sec):	0.0
LM m/z-Correction (ppm):	0.00
=== Ion Optics Settings:	NULL
S-Lens RF Level:	40.00
S-Lens Voltage (V):	21.00
Skimmer Voltage (V):	15.00
Inject Flatapole Offset (V):	5.00
Bent Flatapole DC (V):	2.00
MP2 and MP3 RF (V):	900.00
Gate Lens Voltage (V):	2.25
C-Trap RF (V):	2400.0
====  Diagnostic Data:	NULL
Dynamic RT Shift (min):	0.00
Intens Comp Factor:	1.4281
Res. Dep. Intens:	0.981
CTCD NumF:	0
CTCD Comp:	1.009
CTCD ScScr:	0.844
RawOvFtT:	2378645.5
LC FWHM parameter:	15.0
Rod:	0
PS Inj. Time (ms):	0.640
AGC PS Mode:	1
AGC PS Diag:	3501800
HCD Energy eV:	0.000
AGC Fill:	0.76
Injection t0:	-0.071
t0 FLP:	355.07
Access Id:	0
Analog Input 1 (V):	0.000
Analog Input 2 (V):	0.000
Total Ion Current:	 78725448
Scan Low Mass:	 350
Scan High Mass:	 1800
Scan Start Time (min):	 0.001619751
Scan Number:	 1
Base Peak Intensity:	 5979308
Base Peak Mass:	 445.1181
Scan Mode:	 FTMS + c NSI Full ms [350.0000-1800.0000]
XIC generated from sample.raw consisting of 27 data points.
   Filter : ms
   m/z : 445.1181
   Tolerance : 10 ppm
   RT : 0.001619751 - 0.7801059 min
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 94 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-EH4547.R:12:5'): check tic of EH4547 ───────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub() at test-EH4547.R:12:5
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 94 ]
Error:
! Test failures.
Execution halted