| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:15 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1301/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.11.2 (landing page) Christian Panse
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the MsBackendRawFileReader package: - 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: 1.11.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.11.2.tar.gz |
| StartedAt: 2024-05-19 20:05:42 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 20:09:26 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 223.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendRawFileReader.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.11.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.11.2’
* 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 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 45.551 12.297 21.843
MsBackendRawFileReader 6.236 2.407 12.678
hidden_aliases 5.903 2.350 4.193
MsBackendRawFileReader-class 4.046 1.247 5.438
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 [5.0s]
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠸ | 14 | spectra_subsetting
⠇ | 29 | spectra_subsetting
⠹ | 43 | spectra_subsetting
⠋ | 61 | spectra_subsetting
⠧ | 78 | spectra_subsetting
⠋ | 91 | spectra_subsetting
⠴ | 106 | spectra_subsetting
⠙ | 122 | spectra_subsetting
⠇ | 139 | spectra_subsetting
⠸ | 154 | spectra_subsetting
⠇ | 169 | spectra_subsetting
⠸ | 184 | spectra_subsetting
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⠧ | 228 | spectra_subsetting
⠙ | 242 | spectra_subsetting
⠴ | 256 | spectra_subsetting
⠋ | 271 | spectra_subsetting
⠇ | 289 | spectra_subsetting
⠋ | 311 | spectra_subsetting
⠏ | 320 | spectra_subsetting
⠸ | 334 | spectra_subsetting
⠏ | 350 | spectra_subsetting
⠹ | 373 | spectra_subsetting
⠦ | 387 | spectra_subsetting
⠙ | 402 | spectra_subsetting
⠴ | 416 | spectra_subsetting
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⠧ | 448 | spectra_subsetting
⠸ | 464 | spectra_subsetting
⠋ | 481 | spectra_subsetting
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⠋ | 541 | spectra_subsetting
⠇ | 559 | spectra_subsetting
⠸ | 574 | spectra_subsetting
⠇ | 589 | spectra_subsetting
⠼ | 605 | spectra_subsetting
⠙ | 622 | spectra_subsetting
⠦ | 637 | spectra_subsetting
⠙ | 652 | spectra_subsetting
⠦ | 667 | spectra_subsetting
⠙ | 682 | spectra_subsetting
⠧ | 698 | spectra_subsetting
⠙ | 712 | spectra_subsetting
⠇ | 729 | spectra_subsetting
⠼ | 745 | spectra_subsetting
⠙ | 762 | spectra_subsetting
⠼ | 775 | spectra_subsetting
⠋ | 791 | spectra_subsetting
⠴ | 806 | spectra_subsetting
⠋ | 821 | spectra_subsetting
⠼ | 835 | spectra_subsetting
⠏ | 850 | spectra_subsetting
⠼ | 865 | spectra_subsetting
⠏ | 880 | spectra_subsetting
⠹ | 893 | spectra_subsetting
⠧ | 908 | spectra_subsetting
⠙ | 922 | spectra_subsetting
⠦ | 937 | spectra_subsetting
⠙ | 952 | spectra_subsetting
⠦ | 967 | spectra_subsetting
⠙ | 982 | spectra_subsetting
⠧ | 998 | spectra_subsetting
⠹ | 1013 | spectra_subsetting
⠦ | 1027 | spectra_subsetting
⠙ | 1042 | spectra_subsetting
⠦ | 1057 | spectra_subsetting
⠙ | 1072 | spectra_subsetting
⠼ | 1085 | spectra_subsetting
⠇ | 1099 | spectra_subsetting
⠸ | 1114 | spectra_subsetting
⠇ | 1129 | spectra_subsetting
⠋ | 1141 | spectra_subsetting
⠴ | 1156 | spectra_subsetting
⠙ | 1172 | spectra_subsetting
⠦ | 1187 | spectra_subsetting
⠙ | 1202 | spectra_subsetting
⠸ | 1214 | spectra_subsetting
⠧ | 1228 | spectra_subsetting
⠹ | 1243 | spectra_subsetting
⠧ | 1258 | spectra_subsetting
⠏ | 1270 | spectra_subsetting
⠸ | 1284 | spectra_subsetting
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⠋ | 1411 | spectra_subsetting
⠴ | 1426 | spectra_subsetting
⠋ | 1441 | spectra_subsetting
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⠏ | 1610 | spectra_subsetting
⠦ | 1627 | spectra_subsetting
⠙ | 1642 | spectra_subsetting
⠦ | 1657 | spectra_subsetting
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⠙ | 2012 | spectra_subsetting
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⠧ | 2018 | spectra_subsetting
⠏ | 2020 | spectra_subsetting
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⠴ | 2196 | spectra_subsetting
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⠧ | 2278 | spectra_subsetting
⠋ | 2281 | spectra_subsetting
⠸ | 2284 | spectra_subsetting
⠴ | 2286 | spectra_subsetting
⠇ | 2289 | spectra_subsetting
⠙ | 2292 | spectra_subsetting
⠼ | 2295 | spectra_subsetting
⠧ | 2298 | spectra_subsetting
⠏ | 2300 | spectra_subsetting
⠼ | 2305 | spectra_subsetting
⠹ | 2313 | spectra_subsetting
⠦ | 2317 | spectra_subsetting
✔ | 2317 | spectra_subsetting [41.8s]
⠏ | 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 62 | spectra_variables [18.1s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 64.8 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
92.614 13.474 106.314
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 4.046 | 1.247 | 5.438 | |
| MsBackendRawFileReader | 6.236 | 2.407 | 12.678 | |
| hidden_aliases | 5.903 | 2.350 | 4.193 | |
| ioBenchmark | 45.551 | 12.297 | 21.843 | |