Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:40:48 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1343/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendRawFileReader 1.10.0  (landing page)
Christian Panse
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/MsBackendRawFileReader
git_branch: RELEASE_3_19
git_last_commit: 20a8ce8
git_last_commit_date: 2024-04-30 11:38:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for MsBackendRawFileReader on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MsBackendRawFileReader
Version: 1.10.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MsBackendRawFileReader_1.10.0.tar.gz
StartedAt: 2024-05-04 09:48:20 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 09:52:17 -0000 (Sat, 04 May 2024)
EllapsedTime: 236.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendRawFileReader.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.10.0’
* 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            39.250  3.547  17.997
MsBackendRawFileReader  6.074  1.161   6.645
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MsBackendRawFileReader.Rcheck/00check.log’
for details.


Installation output

MsBackendRawFileReader.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL MsBackendRawFileReader
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)

Tests output

MsBackendRawFileReader.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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

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⠧ |        1978 | spectra_subsetting                                            
⠏ |        1980 | spectra_subsetting                                            
⠙ |        1982 | spectra_subsetting                                            
⠸ |        1984 | spectra_subsetting                                            
⠼ |        1985 | spectra_subsetting                                            
⠦ |        1987 | spectra_subsetting                                            
⠇ |        1989 | spectra_subsetting                                            
⠋ |        1991 | spectra_subsetting                                            
⠹ |        1993 | spectra_subsetting                                            
⠼ |        1995 | spectra_subsetting                                            
⠦ |        1997 | spectra_subsetting                                            
⠇ |        1999 | spectra_subsetting                                            
⠋ |        2001 | spectra_subsetting                                            
⠹ |        2003 | spectra_subsetting                                            
⠼ |        2005 | spectra_subsetting                                            
⠴ |        2006 | spectra_subsetting                                            
⠧ |        2008 | spectra_subsetting                                            
⠏ |        2010 | spectra_subsetting                                            
⠙ |        2012 | spectra_subsetting                                            
⠹ |        2013 | spectra_subsetting                                            
⠼ |        2015 | spectra_subsetting                                            
⠦ |        2017 | spectra_subsetting                                            
⠇ |        2019 | spectra_subsetting                                            
⠏ |        2020 | spectra_subsetting                                            
⠙ |        2022 | spectra_subsetting                                            
⠸ |        2024 | spectra_subsetting                                            
⠴ |        2026 | spectra_subsetting                                            
⠧ |        2028 | spectra_subsetting                                            
⠏ |        2030 | spectra_subsetting                                            
⠙ |        2032 | spectra_subsetting                                            
⠸ |        2034 | spectra_subsetting                                            
⠴ |        2036 | spectra_subsetting                                            
⠧ |        2038 | spectra_subsetting                                            
⠏ |        2040 | spectra_subsetting                                            
⠙ |        2042 | spectra_subsetting                                            
⠸ |        2044 | spectra_subsetting                                            
⠴ |        2046 | spectra_subsetting                                            
⠧ |        2048 | spectra_subsetting                                            
⠏ |        2050 | spectra_subsetting                                            
⠙ |        2052 | spectra_subsetting                                            
⠸ |        2054 | spectra_subsetting                                            
⠴ |        2056 | spectra_subsetting                                            
⠧ |        2058 | spectra_subsetting                                            
⠏ |        2060 | spectra_subsetting                                            
⠙ |        2062 | spectra_subsetting                                            
⠸ |        2064 | spectra_subsetting                                            
⠴ |        2066 | spectra_subsetting                                            
⠧ |        2068 | spectra_subsetting                                            
⠏ |        2070 | spectra_subsetting                                            
⠙ |        2072 | spectra_subsetting                                            
⠸ |        2074 | spectra_subsetting                                            
⠴ |        2076 | spectra_subsetting                                            
⠧ |        2078 | spectra_subsetting                                            
⠏ |        2080 | spectra_subsetting                                            
⠙ |        2082 | spectra_subsetting                                            
⠸ |        2084 | spectra_subsetting                                            
⠴ |        2086 | spectra_subsetting                                            
⠧ |        2088 | spectra_subsetting                                            
⠇ |        2089 | spectra_subsetting                                            
⠋ |        2091 | spectra_subsetting                                            
⠹ |        2093 | spectra_subsetting                                            
⠼ |        2095 | spectra_subsetting                                            
⠦ |        2097 | spectra_subsetting                                            
⠇ |        2099 | spectra_subsetting                                            
⠋ |        2101 | spectra_subsetting                                            
⠹ |        2103 | spectra_subsetting                                            
⠼ |        2105 | spectra_subsetting                                            
⠦ |        2107 | spectra_subsetting                                            
⠇ |        2109 | spectra_subsetting                                            
⠋ |        2111 | spectra_subsetting                                            
⠹ |        2113 | spectra_subsetting                                            
⠼ |        2115 | spectra_subsetting                                            
⠦ |        2117 | spectra_subsetting                                            
⠇ |        2119 | spectra_subsetting                                            
⠋ |        2121 | spectra_subsetting                                            
⠹ |        2123 | spectra_subsetting                                            
⠼ |        2125 | spectra_subsetting                                            
⠦ |        2127 | spectra_subsetting                                            
⠇ |        2129 | spectra_subsetting                                            
⠋ |        2131 | spectra_subsetting                                            
⠹ |        2133 | spectra_subsetting                                            
⠼ |        2135 | spectra_subsetting                                            
⠦ |        2137 | spectra_subsetting                                            
⠇ |        2139 | spectra_subsetting                                            
⠋ |        2141 | spectra_subsetting                                            
⠹ |        2143 | spectra_subsetting                                            
⠼ |        2145 | spectra_subsetting                                            
⠦ |        2147 | spectra_subsetting                                            
⠇ |        2149 | spectra_subsetting                                            
⠋ |        2151 | spectra_subsetting                                            
⠹ |        2153 | spectra_subsetting                                            
⠼ |        2155 | spectra_subsetting                                            
⠦ |        2157 | spectra_subsetting                                            
⠇ |        2159 | spectra_subsetting                                            
⠋ |        2161 | spectra_subsetting                                            
⠹ |        2163 | spectra_subsetting                                            
⠼ |        2165 | spectra_subsetting                                            
⠦ |        2167 | spectra_subsetting                                            
⠇ |        2169 | spectra_subsetting                                            
⠋ |        2171 | spectra_subsetting                                            
⠹ |        2173 | spectra_subsetting                                            
⠼ |        2175 | spectra_subsetting                                            
⠦ |        2177 | spectra_subsetting                                            
⠇ |        2179 | spectra_subsetting                                            
⠋ |        2181 | spectra_subsetting                                            
⠹ |        2183 | spectra_subsetting                                            
⠼ |        2185 | spectra_subsetting                                            
⠦ |        2187 | spectra_subsetting                                            
⠇ |        2189 | spectra_subsetting                                            
⠋ |        2191 | spectra_subsetting                                            
⠹ |        2193 | spectra_subsetting                                            
⠼ |        2195 | spectra_subsetting                                            
⠦ |        2197 | spectra_subsetting                                            
⠇ |        2199 | spectra_subsetting                                            
⠋ |        2201 | spectra_subsetting                                            
⠹ |        2203 | spectra_subsetting                                            
⠼ |        2205 | spectra_subsetting                                            
⠴ |        2206 | spectra_subsetting                                            
⠧ |        2208 | spectra_subsetting                                            
⠏ |        2210 | spectra_subsetting                                            
⠙ |        2212 | spectra_subsetting                                            
⠸ |        2214 | spectra_subsetting                                            
⠴ |        2216 | spectra_subsetting                                            
⠧ |        2218 | spectra_subsetting                                            
⠏ |        2220 | spectra_subsetting                                            
⠙ |        2222 | spectra_subsetting                                            
⠸ |        2224 | spectra_subsetting                                            
⠴ |        2226 | spectra_subsetting                                            
⠧ |        2228 | spectra_subsetting                                            
⠏ |        2230 | spectra_subsetting                                            
⠙ |        2232 | spectra_subsetting                                            
⠸ |        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                                            
⠙ |        2272 | spectra_subsetting                                            
⠸ |        2274 | spectra_subsetting                                            
⠴ |        2276 | spectra_subsetting                                            
⠧ |        2278 | spectra_subsetting                                            
⠏ |        2280 | spectra_subsetting                                            
⠙ |        2282 | spectra_subsetting                                            
⠸ |        2284 | spectra_subsetting                                            
⠴ |        2286 | spectra_subsetting                                            
⠧ |        2288 | spectra_subsetting                                            
⠏ |        2290 | spectra_subsetting                                            
⠙ |        2292 | spectra_subsetting                                            
⠸ |        2294 | spectra_subsetting                                            
⠴ |        2296 | spectra_subsetting                                            
⠧ |        2298 | spectra_subsetting                                            
⠏ |        2300 | spectra_subsetting                                            
⠹ |        2303 | spectra_subsetting                                            
⠴ |        2306 | spectra_subsetting                                            
⠙ |        2312 | spectra_subsetting                                            
⠦ |        2317 | spectra_subsetting                                            
✔ |        2317 | spectra_subsetting [65.9s]

⠏ |          0 | spectra_variables                                              
⠙ |         12 | spectra_variables                                              
⠸ |         14 | spectra_variables                                              
⠴ |         16 | spectra_variables                                              
⠙ |         32 | spectra_variables                                              
⠹ |         43 | spectra_variables                                              
⠴ |      1  55 | spectra_variables                                              
✔ |      1  62 | spectra_variables [10.4s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 81.4 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 
115.241   7.254 120.340 

Example timings

MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings

nameusersystemelapsed
MsBackendRawFileReader-class4.3740.5624.889
MsBackendRawFileReader6.0741.1616.645
hidden_aliases2.8490.5693.137
ioBenchmark39.250 3.54717.997