| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:41 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the rawrr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rawrr.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 1604/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rawrr 1.9.0 (landing page) Christian Panse
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: rawrr |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:rawrr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings rawrr_1.9.0.tar.gz |
| StartedAt: 2023-05-30 16:21:05 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 16:23:14 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 129.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rawrr.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:rawrr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings rawrr_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rawrr.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 ‘rawrr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawrr’ version ‘1.9.0’
* 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 ‘rawrr’ 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
readChromatogram 15.369 4.770 18.642
readSpectrum 13.386 2.069 15.884
* 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 ...
‘rawrr.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
rawrr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL rawrr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘rawrr’ ... ** 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 (rawrr)
rawrr.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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.
> #R
>
> library(testthat)
>
> suppressPackageStartupMessages(library(rawrr))
>
> test_check("rawrr")
Total Ion Current: 78725448
Scan Low Mass: 350
Scan High Mass: 1800
Scan Start Time (min): 0.001619751
Scan Number: 1
Base Peak Intensity: 5979308
Base Peak Mass: 445.1181
Scan Mode: FTMS + c NSI Full ms [350.0000-1800.0000]
======= Instrument data ===== : NULL
Multiple Injection: ii
Multi Inject Info: IT=28;28
AGC: On
Micro Scan Count: 1
Scan Segment: 1
Scan Event: 1
Master Index: 0
Charge State: 0
Monoisotopic M/Z: 0.0000
Ion Injection Time (ms): 55.000
Max. Ion Time (ms): 55.00
FT Resolution: 120000
MS2 Isolation Width: 1450.00
MS2 Isolation Offset: 0.00
AGC Target: 3000000
HCD Energy:
Analyzer Temperature: 27.06
=== Mass Calibration: NULL
Conversion Parameter B: 211820589.2896
Conversion Parameter C: -41163067.8349
Temperature Comp. (ppm): -2.35
RF Comp. (ppm): -0.09
Space Charge Comp. (ppm): -2.30
Resolution Comp. (ppm): 0.57
Number of Lock Masses: 0
Lock Mass #1 (m/z): 0.0000
Lock Mass #2 (m/z): 0.0000
Lock Mass #3 (m/z): 0.0000
LM Search Window (ppm): 0.0
LM Search Window (mmu): 0.0
Number of LM Found: 0
Last Locking (sec): 0.0
LM m/z-Correction (ppm): 0.00
=== Ion Optics Settings: NULL
S-Lens RF Level: 40.00
S-Lens Voltage (V): 21.00
Skimmer Voltage (V): 15.00
Inject Flatapole Offset (V): 5.00
Bent Flatapole DC (V): 2.00
MP2 and MP3 RF (V): 900.00
Gate Lens Voltage (V): 2.25
C-Trap RF (V): 2400.0
==== Diagnostic Data: NULL
Dynamic RT Shift (min): 0.00
Intens Comp Factor: 1.4281
Res. Dep. Intens: 0.981
CTCD NumF: 0
CTCD Comp: 1.009
CTCD ScScr: 0.844
RawOvFtT: 2378645.5
LC FWHM parameter: 15.0
Rod: 0
PS Inj. Time (ms): 0.640
AGC PS Mode: 1
AGC PS Diag: 3501800
HCD Energy eV: 0.000
AGC Fill: 0.76
Injection t0: -0.071
t0 FLP: 355.07
Access Id: 0
Analog Input 1 (V): 0.000
Analog Input 2 (V): 0.000
Total Ion Current: 78725448
Scan Low Mass: 350
Scan High Mass: 1800
Scan Start Time (min): 0.001619751
Scan Number: 1
Base Peak Intensity: 5979308
Base Peak Mass: 445.1181
Scan Mode: FTMS + c NSI Full ms [350.0000-1800.0000]
XIC generated from sample.raw consisting of 27 data points.
Filter : ms
m/z : 445.1181
Tolerance : 10 ppm
RT : 0.001619751 - 0.7801059 min
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 178 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 178 ]
>
> proc.time()
user system elapsed
16.676 3.511 21.624
rawrr.Rcheck/rawrr-Ex.timings
| name | user | system | elapsed | |
| basePeak | 0.299 | 0.058 | 0.302 | |
| dependentScan | 0.314 | 0.113 | 0.365 | |
| faimsVoltageOn | 0.250 | 0.102 | 0.299 | |
| installRawFileReaderDLLs | 0 | 0 | 0 | |
| is.rawrrChromatogram | 0.300 | 0.111 | 0.332 | |
| is.rawrrSpectrum | 0.284 | 0.066 | 0.292 | |
| is.rawrrSpectrumSet | 0.299 | 0.055 | 0.298 | |
| makeAccessor | 0.251 | 0.090 | 0.286 | |
| massRange | 0.263 | 0.085 | 0.286 | |
| masterScan | 0.326 | 0.102 | 0.366 | |
| plot.rawrrChromatogram | 0.284 | 0.147 | 0.321 | |
| rawrrAssemblyPath | 0.000 | 0.000 | 0.001 | |
| rawrrSpectrum | 0.026 | 0.000 | 0.025 | |
| readChromatogram | 15.369 | 4.770 | 18.642 | |
| readFileHeader | 0.191 | 0.080 | 0.238 | |
| readIndex | 0.355 | 0.061 | 0.361 | |
| readSpectrum | 13.386 | 2.069 | 15.884 | |
| readTrailer | 0.433 | 0.139 | 0.477 | |
| sampleFilePath | 0.001 | 0.000 | 0.001 | |
| scanNumber | 0.250 | 0.127 | 0.296 | |
| summary.rawrrChromatogram | 0.276 | 0.132 | 0.309 | |
| tic | 0.257 | 0.057 | 0.268 | |
| validate_rawrrIndex | 0.385 | 0.040 | 0.377 | |
| validate_rawrrSpectrum | 0.238 | 0.090 | 0.280 | |