| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:35 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 1276/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.7.0 (landing page) Christian Panse
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: MsBackendRawFileReader |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2023-05-09 22:13:33 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 22:20:14 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 400.5 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-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 ‘1.7.0’
* 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 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 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 41.036 5.098 20.736
MsBackendRawFileReader 6.053 1.489 6.739
* 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-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
⠹ | 13 | spectra_subsetting
⠼ | 25 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠦ | 47 | spectra_subsetting
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⠋ | 91 | spectra_subsetting
⠹ | 103 | spectra_subsetting
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⠴ | 136 | spectra_subsetting
⠧ | 148 | spectra_subsetting
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⠙ | 172 | spectra_subsetting
⠹ | 183 | spectra_subsetting
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⠏ | 250 | spectra_subsetting
⠙ | 262 | spectra_subsetting
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⠹ | 283 | spectra_subsetting
⠼ | 295 | spectra_subsetting
⠦ | 307 | spectra_subsetting
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⠙ | 352 | spectra_subsetting
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⠼ | 385 | spectra_subsetting
⠦ | 397 | spectra_subsetting
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⠋ | 571 | spectra_subsetting
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⠇ | 629 | spectra_subsetting
⠏ | 640 | spectra_subsetting
⠙ | 652 | spectra_subsetting
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⠹ | 673 | spectra_subsetting
⠼ | 685 | spectra_subsetting
⠦ | 697 | spectra_subsetting
⠇ | 709 | spectra_subsetting
⠋ | 721 | spectra_subsetting
⠹ | 733 | spectra_subsetting
⠼ | 745 | spectra_subsetting
⠦ | 757 | spectra_subsetting
⠦ | 767 | spectra_subsetting
⠧ | 778 | spectra_subsetting
⠏ | 790 | spectra_subsetting
⠙ | 802 | spectra_subsetting
⠙ | 812 | spectra_subsetting
⠹ | 823 | spectra_subsetting
⠼ | 835 | spectra_subsetting
⠦ | 847 | spectra_subsetting
⠇ | 859 | spectra_subsetting
⠏ | 870 | spectra_subsetting
⠏ | 880 | spectra_subsetting
⠙ | 892 | spectra_subsetting
⠸ | 904 | spectra_subsetting
⠸ | 914 | spectra_subsetting
⠼ | 925 | spectra_subsetting
⠦ | 937 | spectra_subsetting
⠇ | 949 | spectra_subsetting
⠇ | 959 | spectra_subsetting
⠏ | 970 | spectra_subsetting
⠙ | 982 | spectra_subsetting
⠸ | 994 | spectra_subsetting
⠴ | 1006 | spectra_subsetting
⠴ | 1016 | spectra_subsetting
⠦ | 1027 | spectra_subsetting
⠇ | 1039 | spectra_subsetting
⠋ | 1051 | spectra_subsetting
⠋ | 1061 | spectra_subsetting
⠙ | 1072 | spectra_subsetting
⠸ | 1084 | spectra_subsetting
⠴ | 1096 | spectra_subsetting
⠧ | 1108 | spectra_subsetting
⠏ | 1120 | spectra_subsetting
⠙ | 1132 | spectra_subsetting
⠸ | 1144 | spectra_subsetting
⠴ | 1156 | spectra_subsetting
⠴ | 1166 | spectra_subsetting
⠦ | 1177 | spectra_subsetting
⠇ | 1189 | spectra_subsetting
⠋ | 1201 | spectra_subsetting
⠏ | 1210 | spectra_subsetting
⠙ | 1222 | spectra_subsetting
⠸ | 1234 | spectra_subsetting
⠴ | 1246 | spectra_subsetting
⠴ | 1256 | spectra_subsetting
⠼ | 1265 | spectra_subsetting
⠴ | 1276 | spectra_subsetting
⠧ | 1288 | spectra_subsetting
⠏ | 1300 | spectra_subsetting
⠇ | 1309 | spectra_subsetting
⠋ | 1321 | spectra_subsetting
⠹ | 1333 | spectra_subsetting
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⠏ | 1690 | spectra_subsetting
⠙ | 1702 | spectra_subsetting
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⠸ | 2234 | spectra_subsetting
⠴ | 2236 | spectra_subsetting
⠧ | 2238 | spectra_subsetting
⠏ | 2240 | spectra_subsetting
⠙ | 2242 | spectra_subsetting
⠸ | 2244 | spectra_subsetting
⠴ | 2246 | spectra_subsetting
⠧ | 2248 | spectra_subsetting
⠏ | 2250 | spectra_subsetting
⠙ | 2252 | spectra_subsetting
⠸ | 2254 | spectra_subsetting
⠴ | 2256 | spectra_subsetting
⠧ | 2258 | spectra_subsetting
⠏ | 2260 | spectra_subsetting
⠙ | 2262 | spectra_subsetting
⠸ | 2264 | spectra_subsetting
⠴ | 2266 | spectra_subsetting
⠧ | 2268 | spectra_subsetting
⠏ | 2270 | spectra_subsetting
⠋ | 2271 | spectra_subsetting
⠹ | 2273 | spectra_subsetting
⠼ | 2275 | spectra_subsetting
⠦ | 2277 | spectra_subsetting
⠇ | 2279 | spectra_subsetting
⠋ | 2281 | spectra_subsetting
⠹ | 2283 | spectra_subsetting
⠼ | 2285 | spectra_subsetting
⠦ | 2287 | spectra_subsetting
⠇ | 2289 | spectra_subsetting
⠋ | 2291 | spectra_subsetting
⠹ | 2293 | spectra_subsetting
⠼ | 2295 | spectra_subsetting
⠇ | 2299 | spectra_subsetting
⠹ | 2303 | spectra_subsetting
⠇ | 2309 | spectra_subsetting
⠹ | 2313 | spectra_subsetting
✔ | 2313 | spectra_subsetting [62.7s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠹ | 43 | spectra_variables
⠋ | 1 60 | spectra_variables
✔ | 1 62 | spectra_variables [10.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_spectra_variables.R:262:1'): spectraNames
Reason: empty test
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 73.1 s
── Skipped tests ──────────────────────────────────────────────────────────────
• empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2375 ]
>
> proc.time()
user system elapsed
107.304 6.069 110.556
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 3.947 | 0.815 | 4.560 | |
| MsBackendRawFileReader | 6.053 | 1.489 | 6.739 | |
| hidden_aliases | 2.862 | 0.671 | 3.164 | |
| ioBenchmark | 41.036 | 5.098 | 20.736 | |