| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:05 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 1343/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.10.0 (landing page) Christian Panse
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsBackendRawFileReader_1.10.0.tar.gz |
| StartedAt: 2024-05-31 05:51:16 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 05:56:25 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 308.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendRawFileReader.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsBackendRawFileReader_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.10.0’
* 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 ... NOTE
filterScan,MsBackendRawFileReader : <anonymous>: no visible global
function definition for ‘scanIndex’
peaksData,MsBackendRawFileReader: no visible global function definition
for ‘scanIndex’
Undefined global functions or variables:
scanIndex
* 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 59.853 4.263 12.744
MsBackendRawFileReader 5.345 0.955 5.666
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/MsBackendRawFileReader.Rcheck/00check.log’
for details.
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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
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 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 [3.8s]
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠇ | 19 | spectra_subsetting
⠴ | 36 | spectra_subsetting
⠹ | 53 | spectra_subsetting
⠏ | 70 | spectra_subsetting
⠧ | 88 | spectra_subsetting
⠴ | 106 | spectra_subsetting
⠸ | 124 | spectra_subsetting
⠙ | 142 | spectra_subsetting
⠦ | 157 | spectra_subsetting
⠼ | 175 | spectra_subsetting
⠹ | 193 | spectra_subsetting
⠋ | 211 | spectra_subsetting
⠇ | 229 | spectra_subsetting
⠦ | 247 | spectra_subsetting
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⠹ | 283 | spectra_subsetting
⠋ | 301 | spectra_subsetting
⠇ | 319 | spectra_subsetting
⠋ | 331 | spectra_subsetting
⠇ | 349 | spectra_subsetting
⠦ | 367 | spectra_subsetting
⠼ | 385 | spectra_subsetting
⠦ | 397 | spectra_subsetting
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⠋ | 431 | spectra_subsetting
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⠇ | 499 | spectra_subsetting
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⠏ | 550 | spectra_subsetting
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⠴ | 586 | spectra_subsetting
⠙ | 602 | spectra_subsetting
⠇ | 619 | spectra_subsetting
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⠼ | 655 | spectra_subsetting
⠹ | 673 | spectra_subsetting
⠋ | 691 | spectra_subsetting
⠦ | 707 | spectra_subsetting
⠋ | 721 | spectra_subsetting
⠇ | 739 | spectra_subsetting
⠦ | 757 | spectra_subsetting
⠼ | 775 | spectra_subsetting
⠋ | 791 | spectra_subsetting
⠧ | 808 | spectra_subsetting
⠴ | 826 | spectra_subsetting
⠸ | 844 | spectra_subsetting
⠙ | 862 | spectra_subsetting
⠏ | 880 | spectra_subsetting
⠧ | 898 | spectra_subsetting
⠴ | 916 | spectra_subsetting
⠸ | 934 | spectra_subsetting
⠙ | 952 | spectra_subsetting
⠏ | 970 | spectra_subsetting
⠙ | 982 | spectra_subsetting
⠏ | 1000 | spectra_subsetting
⠧ | 1018 | spectra_subsetting
⠴ | 1036 | spectra_subsetting
⠙ | 1052 | spectra_subsetting
⠇ | 1069 | spectra_subsetting
⠦ | 1087 | spectra_subsetting
⠼ | 1105 | spectra_subsetting
⠋ | 1121 | spectra_subsetting
⠧ | 1138 | spectra_subsetting
⠴ | 1156 | spectra_subsetting
⠸ | 1174 | spectra_subsetting
⠏ | 1190 | spectra_subsetting
⠦ | 1207 | spectra_subsetting
⠸ | 1224 | spectra_subsetting
⠏ | 1240 | spectra_subsetting
⠧ | 1258 | spectra_subsetting
⠴ | 1276 | spectra_subsetting
⠸ | 1294 | spectra_subsetting
⠏ | 1310 | spectra_subsetting
⠦ | 1327 | spectra_subsetting
⠼ | 1345 | spectra_subsetting
⠹ | 1363 | spectra_subsetting
⠧ | 1378 | spectra_subsetting
⠴ | 1396 | spectra_subsetting
⠸ | 1414 | spectra_subsetting
⠙ | 1432 | spectra_subsetting
⠏ | 1450 | spectra_subsetting
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⠴ | 1486 | spectra_subsetting
⠹ | 1503 | spectra_subsetting
⠇ | 1519 | spectra_subsetting
⠦ | 1537 | spectra_subsetting
⠼ | 1555 | spectra_subsetting
⠙ | 1572 | spectra_subsetting
⠧ | 1588 | spectra_subsetting
⠴ | 1606 | spectra_subsetting
⠸ | 1624 | spectra_subsetting
⠙ | 1642 | spectra_subsetting
⠏ | 1660 | spectra_subsetting
⠧ | 1678 | spectra_subsetting
⠹ | 1693 | spectra_subsetting
⠋ | 1711 | spectra_subsetting
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⠹ | 2303 | spectra_subsetting
⠇ | 2309 | spectra_subsetting
⠦ | 2317 | spectra_subsetting
✔ | 2317 | spectra_subsetting [40.6s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠹ | 43 | spectra_variables
⠹ | 1 62 | spectra_variables
✔ | 1 62 | spectra_variables [8.3s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 52.7 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2383 ]
>
> proc.time()
user system elapsed
81.484 5.244 84.605
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 3.845 | 0.770 | 4.442 | |
| MsBackendRawFileReader | 5.345 | 0.955 | 5.666 | |
| hidden_aliases | 2.502 | 0.434 | 2.654 | |
| ioBenchmark | 59.853 | 4.263 | 12.744 | |