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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1632/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rawrr 1.8.1  (landing page)
Christian Panse
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/rawrr
git_branch: RELEASE_3_17
git_last_commit: 0ed410e
git_last_commit_date: 2023-05-09 09:46:58 -0400 (Tue, 09 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for rawrr on kjohnson2


To the developers/maintainers of the rawrr 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.

raw results


Summary

Package: rawrr
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rawrr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rawrr_1.8.1.tar.gz
StartedAt: 2023-10-18 17:23:25 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:25:49 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 144.4 seconds
RetCode: 0
Status:   OK  
CheckDir: rawrr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rawrr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rawrr_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rawrr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rawrr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawrr’ version ‘1.8.1’
* 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 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 15.19  3.206  29.448
readSpectrum     12.01  1.477  21.679
* 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


Installation output

rawrr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rawrr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output

rawrr.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
 16.561   3.070  33.895 

Example timings

rawrr.Rcheck/rawrr-Ex.timings

nameusersystemelapsed
basePeak0.3110.1321.478
dependentScan0.3250.0850.942
faimsVoltageOn0.2830.0830.843
installRawFileReaderDLLs000
is.rawrrChromatogram0.3080.0900.919
is.rawrrSpectrum0.2790.0780.752
is.rawrrSpectrumSet0.2840.0780.857
makeAccessor0.2820.0830.897
massRange0.270.080.88
masterScan0.3390.0930.777
plot.rawrrChromatogram0.2960.0860.689
rawrrAssemblyPath0.0010.0000.000
rawrrSpectrum0.0190.0010.029
readChromatogram15.190 3.20629.448
readFileHeader0.2420.0790.637
readIndex0.3410.0950.747
readSpectrum12.010 1.47721.679
readTrailer0.4630.1641.621
sampleFilePath0.0020.0000.002
scanNumber0.2930.0910.896
summary.rawrrChromatogram0.3190.0890.994
tic0.2780.0860.858
validate_rawrrIndex0.3490.1201.033
validate_rawrrSpectrum0.2940.0840.909