| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:27 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1286/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.5.5 (landing page) Christian Panse
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: MsBackendRawFileReader |
| Version: 1.5.5 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MsBackendRawFileReader_1.5.5.tar.gz |
| StartedAt: 2023-04-11 21:47:08 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 21:52:31 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 322.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendRawFileReader.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MsBackendRawFileReader_1.5.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.5.5’
* 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 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 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 43.952 4.727 13.419
MsBackendRawFileReader 5.311 0.931 5.510
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MsBackendRawFileReader.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: BiocParallel
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
> 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 20 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• isFALSE(file.exists(sample_mzXML_file)) is TRUE (1)
• isFALSE(require(MsBackendRawMgf)) is TRUE (1)
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 20 ]
>
>
> 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 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠴ | 16 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠴ | 46 | spectra_subsetting
⠙ | 62 | spectra_subsetting
⠴ | 76 | spectra_subsetting
⠏ | 90 | spectra_subsetting
⠴ | 106 | spectra_subsetting
⠋ | 121 | spectra_subsetting
⠴ | 136 | spectra_subsetting
⠋ | 151 | spectra_subsetting
⠦ | 167 | spectra_subsetting
⠋ | 181 | spectra_subsetting
⠸ | 194 | spectra_subsetting
⠇ | 209 | spectra_subsetting
⠸ | 224 | spectra_subsetting
⠧ | 238 | spectra_subsetting
⠹ | 253 | spectra_subsetting
⠏ | 270 | spectra_subsetting
⠸ | 284 | spectra_subsetting
⠧ | 298 | spectra_subsetting
⠴ | 316 | spectra_subsetting
⠋ | 331 | spectra_subsetting
⠴ | 346 | spectra_subsetting
⠋ | 361 | spectra_subsetting
⠴ | 376 | spectra_subsetting
⠋ | 391 | spectra_subsetting
⠴ | 406 | spectra_subsetting
⠋ | 421 | spectra_subsetting
⠴ | 436 | spectra_subsetting
⠧ | 448 | spectra_subsetting
⠋ | 461 | spectra_subsetting
⠼ | 475 | spectra_subsetting
⠸ | 484 | spectra_subsetting
⠇ | 499 | spectra_subsetting
⠼ | 515 | spectra_subsetting
⠙ | 532 | spectra_subsetting
⠼ | 545 | spectra_subsetting
⠏ | 560 | spectra_subsetting
⠸ | 574 | spectra_subsetting
⠇ | 589 | spectra_subsetting
⠙ | 602 | spectra_subsetting
⠴ | 616 | spectra_subsetting
⠹ | 633 | spectra_subsetting
⠴ | 646 | spectra_subsetting
⠋ | 661 | spectra_subsetting
⠴ | 676 | spectra_subsetting
⠋ | 691 | spectra_subsetting
⠼ | 705 | spectra_subsetting
⠋ | 721 | spectra_subsetting
⠴ | 736 | spectra_subsetting
⠋ | 751 | spectra_subsetting
⠴ | 766 | spectra_subsetting
⠙ | 782 | spectra_subsetting
⠴ | 796 | spectra_subsetting
⠋ | 811 | spectra_subsetting
⠦ | 827 | spectra_subsetting
⠸ | 844 | spectra_subsetting
⠦ | 857 | spectra_subsetting
⠸ | 874 | spectra_subsetting
⠋ | 891 | spectra_subsetting
⠸ | 904 | spectra_subsetting
⠇ | 919 | spectra_subsetting
⠼ | 935 | spectra_subsetting
⠙ | 952 | spectra_subsetting
⠦ | 967 | spectra_subsetting
⠹ | 983 | spectra_subsetting
⠏ | 1000 | spectra_subsetting
⠹ | 1013 | spectra_subsetting
⠧ | 1028 | spectra_subsetting
⠼ | 1045 | spectra_subsetting
⠧ | 1058 | spectra_subsetting
⠙ | 1072 | spectra_subsetting
⠦ | 1087 | spectra_subsetting
⠙ | 1102 | spectra_subsetting
⠸ | 1114 | spectra_subsetting
⠏ | 1130 | spectra_subsetting
⠦ | 1147 | spectra_subsetting
⠙ | 1162 | spectra_subsetting
⠦ | 1177 | spectra_subsetting
⠹ | 1193 | spectra_subsetting
⠧ | 1208 | spectra_subsetting
⠙ | 1222 | spectra_subsetting
⠦ | 1237 | spectra_subsetting
⠹ | 1253 | spectra_subsetting
⠦ | 1267 | spectra_subsetting
⠙ | 1282 | spectra_subsetting
⠦ | 1297 | spectra_subsetting
⠙ | 1312 | spectra_subsetting
⠸ | 1324 | spectra_subsetting
⠇ | 1339 | spectra_subsetting
⠼ | 1355 | spectra_subsetting
⠇ | 1369 | spectra_subsetting
⠸ | 1384 | spectra_subsetting
⠇ | 1399 | spectra_subsetting
⠸ | 1414 | spectra_subsetting
⠇ | 1429 | spectra_subsetting
⠴ | 1446 | spectra_subsetting
⠙ | 1462 | spectra_subsetting
⠼ | 1475 | spectra_subsetting
⠏ | 1490 | spectra_subsetting
⠦ | 1507 | spectra_subsetting
⠙ | 1522 | spectra_subsetting
⠦ | 1537 | spectra_subsetting
⠙ | 1552 | spectra_subsetting
⠦ | 1567 | spectra_subsetting
⠹ | 1583 | spectra_subsetting
⠧ | 1598 | spectra_subsetting
⠹ | 1613 | spectra_subsetting
⠦ | 1627 | spectra_subsetting
⠹ | 1643 | spectra_subsetting
⠏ | 1660 | spectra_subsetting
⠼ | 1675 | spectra_subsetting
⠋ | 1691 | spectra_subsetting
⠼ | 1705 | spectra_subsetting
⠏ | 1720 | spectra_subsetting
⠸ | 1724 | spectra_subsetting
⠴ | 1726 | spectra_subsetting
⠧ | 1728 | spectra_subsetting
⠏ | 1730 | spectra_subsetting
⠙ | 1732 | spectra_subsetting
⠸ | 1734 | spectra_subsetting
⠴ | 1736 | spectra_subsetting
⠧ | 1738 | spectra_subsetting
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⠴ | 1746 | spectra_subsetting
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⠏ | 1750 | spectra_subsetting
⠙ | 1752 | spectra_subsetting
⠸ | 1754 | spectra_subsetting
⠴ | 1756 | spectra_subsetting
⠧ | 1758 | spectra_subsetting
⠏ | 1760 | spectra_subsetting
⠙ | 1762 | spectra_subsetting
⠸ | 1764 | spectra_subsetting
⠴ | 1766 | spectra_subsetting
⠧ | 1768 | spectra_subsetting
⠏ | 1770 | spectra_subsetting
⠙ | 1772 | spectra_subsetting
⠸ | 1774 | spectra_subsetting
⠴ | 1776 | spectra_subsetting
⠧ | 1778 | spectra_subsetting
⠏ | 1780 | spectra_subsetting
⠙ | 1782 | spectra_subsetting
⠸ | 1784 | spectra_subsetting
⠴ | 1786 | spectra_subsetting
⠧ | 1788 | spectra_subsetting
⠏ | 1790 | spectra_subsetting
⠙ | 1792 | spectra_subsetting
⠸ | 1794 | spectra_subsetting
⠴ | 1796 | spectra_subsetting
⠧ | 1798 | spectra_subsetting
⠏ | 1800 | spectra_subsetting
⠙ | 1802 | spectra_subsetting
⠸ | 1804 | spectra_subsetting
⠴ | 1806 | spectra_subsetting
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⠏ | 1810 | spectra_subsetting
⠙ | 1812 | spectra_subsetting
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⠏ | 2070 | spectra_subsetting
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⠏ | 2090 | spectra_subsetting
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⠏ | 2100 | spectra_subsetting
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⠴ | 2136 | spectra_subsetting
⠧ | 2138 | spectra_subsetting
⠏ | 2140 | spectra_subsetting
⠙ | 2142 | spectra_subsetting
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⠏ | 2290 | spectra_subsetting
⠙ | 2292 | spectra_subsetting
⠸ | 2294 | spectra_subsetting
⠴ | 2296 | spectra_subsetting
⠏ | 2300 | spectra_subsetting
⠧ | 2308 | spectra_subsetting
⠹ | 2313 | spectra_subsetting
✔ | 2313 | spectra_subsetting [47.2s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠹ | 43 | spectra_variables
✔ | 1 62 | spectra_variables [8.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_spectra_variables.R:262:1'): spectraNames
Reason: empty test
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 55.6 s
── Skipped tests ──────────────────────────────────────────────────────────────
• empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2375 ]
>
> proc.time()
user system elapsed
85.433 4.706 87.579
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 3.580 | 0.545 | 3.867 | |
| MsBackendRawFileReader | 5.311 | 0.931 | 5.510 | |
| hidden_aliases | 2.594 | 0.527 | 2.734 | |
| ioBenchmark | 43.952 | 4.727 | 13.419 | |