| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:45 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 rawrr package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1581/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rawrr 1.7.0 (landing page) Christian Panse
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: rawrr |
| Version: 1.7.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rawrr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rawrr_1.7.0.tar.gz |
| StartedAt: 2022-12-29 02:37:58 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:39:32 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 94.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rawrr.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rawrr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rawrr_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/rawrr.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rawrr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rawrr' 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 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 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 6.30 1.79 21.58
readSpectrum 2.15 0.21 10.14
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
rawrr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rawrr ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
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
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 s
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 175 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 175 ]
>
> proc.time()
user system elapsed
7.50 1.64 22.23
rawrr.Rcheck/rawrr-Ex.timings
| name | user | system | elapsed | |
| basePeak | 0.04 | 0.02 | 0.81 | |
| dependentScan | 0.00 | 0.00 | 0.56 | |
| faimsVoltageOn | 0.00 | 0.01 | 0.54 | |
| installRawFileReaderDLLs | 0 | 0 | 0 | |
| is.rawrrChromatogram | 0.02 | 0.00 | 0.68 | |
| is.rawrrSpectrum | 0.01 | 0.02 | 0.56 | |
| is.rawrrSpectrumSet | 0.00 | 0.00 | 0.53 | |
| makeAccessor | 0.02 | 0.00 | 0.55 | |
| massRange | 0.00 | 0.00 | 0.64 | |
| masterScan | 0.01 | 0.00 | 0.58 | |
| plot.rawrrChromatogram | 0.02 | 0.02 | 0.60 | |
| rawrrAssemblyPath | 0 | 0 | 0 | |
| rawrrSpectrum | 0.01 | 0.00 | 0.02 | |
| readChromatogram | 6.30 | 1.79 | 21.58 | |
| readFileHeader | 0.0 | 0.0 | 0.5 | |
| readIndex | 0.02 | 0.02 | 0.61 | |
| readSpectrum | 2.15 | 0.21 | 10.14 | |
| sampleFilePath | 0 | 0 | 0 | |
| scanNumber | 0.00 | 0.00 | 0.54 | |
| summary.rawrrChromatogram | 0.00 | 0.00 | 0.59 | |
| tic | 0.00 | 0.01 | 0.55 | |
| validate_rawrrIndex | 0.05 | 0.03 | 0.68 | |