| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-20 12:16 -0500 (Mon, 20 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1333/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.12.0 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the MsBackendRawFileReader package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendRawFileReader.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MsBackendRawFileReader |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendRawFileReader_1.12.0.tar.gz |
| StartedAt: 2025-01-19 22:57:04 -0500 (Sun, 19 Jan 2025) |
| EndedAt: 2025-01-19 23:02:13 -0500 (Sun, 19 Jan 2025) |
| EllapsedTime: 309.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendRawFileReader.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendRawFileReader_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.12.0’
* 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 ‘MsBackendRawFileReader’ 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ioBenchmark 76.073 4.741 13.395
MsBackendRawFileReader 7.342 1.650 8.020
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MsBackendRawFileReader’ ... ** 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 (MsBackendRawFileReader)
MsBackendRawFileReader.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.
> library("testthat")
> library("MsBackendRawFileReader")
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: BiocParallel
> library("Spectra")
>
>
> sample_raw_file <- file.path(system.file(package = "rawrr"),
+ 'extdata', 'sample.raw')
>
> sample_mzXML_file <- file.path(path.package(package = 'MsBackendRawFileReader'),
+ 'extdata', 'sample.mzXML')
>
>
> sample_raw <- backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(), files = sample_raw_file)
>
>
> #sample_mzr <- backendInitialize(MsBackendMzR(), files = sample_mzXML_file)
>
>
> mgf_file <- file.path(system.file(package = "MsBackendRawFileReader"),
+ 'extdata', '3159619b11ed_4590_9594.mgf')
>
>
> rv <- lapply(1:2, function(x){
+ file.copy(from = sample_raw_file, to = tempfile(fileext='.raw'))})
>
>
> register(SnowParam(workers = 1, type = "SOCK") , default = TRUE);
> sample_raw_2 <- backendInitialize(MsBackendRawFileReader(),
+ files = file.path(tempdir(),
+ list.files(path = tempdir(), pattern = 'raw$')))
>
>
> test_check("MsBackendRawFileReader")
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 21 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• isFALSE(file.exists(sample_mzXML_file)) is TRUE (1):
'test_MsBackendMzR_MsBackendRawFileReader.R:1:1'
• isFALSE(require(MsBackendRawMgf)) is TRUE (1): 'test_top_n_mgf.R:1:1'
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 21 ]
>
>
> be <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
+ files = c(sample_raw_file))
>
> ## Run the MsBackend spectra variable test suite
>
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> #res <- test_file(paste0(test_suite, "/test_spectra_variables.R"),
> # reporter = check_reporter(), stop_on_failure = TRUE)
>
>
> ## Run the whole suite.
> res <- test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠙ | 2 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables [4.0s]
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠴ | 16 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠴ | 46 | spectra_subsetting
⠋ | 61 | spectra_subsetting
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⠇ | 89 | spectra_subsetting
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⠴ | 256 | spectra_subsetting
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⠙ | 352 | spectra_subsetting
⠇ | 369 | spectra_subsetting
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⠏ | 400 | spectra_subsetting
⠧ | 418 | spectra_subsetting
⠴ | 436 | spectra_subsetting
⠸ | 454 | spectra_subsetting
⠇ | 469 | spectra_subsetting
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⠇ | 619 | spectra_subsetting
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⠼ | 685 | spectra_subsetting
⠙ | 702 | spectra_subsetting
⠴ | 716 | spectra_subsetting
⠹ | 733 | spectra_subsetting
⠧ | 748 | spectra_subsetting
⠹ | 763 | spectra_subsetting
⠧ | 778 | spectra_subsetting
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⠧ | 808 | spectra_subsetting
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⠋ | 871 | spectra_subsetting
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⠹ | 903 | spectra_subsetting
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⠙ | 932 | spectra_subsetting
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⠋ | 961 | spectra_subsetting
⠦ | 977 | spectra_subsetting
⠙ | 992 | spectra_subsetting
⠇ | 1009 | spectra_subsetting
⠸ | 1024 | spectra_subsetting
⠇ | 1039 | spectra_subsetting
⠼ | 1055 | spectra_subsetting
⠏ | 1070 | spectra_subsetting
⠼ | 1085 | spectra_subsetting
⠇ | 1099 | spectra_subsetting
⠸ | 1114 | spectra_subsetting
⠏ | 1130 | spectra_subsetting
⠼ | 1145 | spectra_subsetting
⠏ | 1160 | spectra_subsetting
⠦ | 1177 | spectra_subsetting
⠙ | 1192 | spectra_subsetting
⠦ | 1207 | spectra_subsetting
⠙ | 1222 | spectra_subsetting
⠇ | 1239 | spectra_subsetting
⠼ | 1255 | spectra_subsetting
⠏ | 1270 | spectra_subsetting
⠼ | 1285 | spectra_subsetting
⠋ | 1301 | spectra_subsetting
⠴ | 1316 | spectra_subsetting
⠋ | 1331 | spectra_subsetting
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⠏ | 1360 | spectra_subsetting
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⠋ | 1391 | spectra_subsetting
⠴ | 1406 | spectra_subsetting
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⠹ | 1453 | spectra_subsetting
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⠏ | 2300 | spectra_subsetting
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⠦ | 2317 | spectra_subsetting
⠸ | 2324 | spectra_subsetting
✔ | 2324 | spectra_subsetting [43.2s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠦ | 27 | spectra_variables
⠇ | 29 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠋ | 1 60 | spectra_variables
✔ | 1 62 | spectra_variables [14.9s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 62.1 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2390 ]
>
> proc.time()
user system elapsed
88.895 6.543 92.850
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 3.207 | 0.590 | 3.532 | |
| MsBackendRawFileReader | 7.342 | 1.650 | 8.020 | |
| hidden_aliases | 2.357 | 0.542 | 2.583 | |
| ioBenchmark | 76.073 | 4.741 | 13.395 | |