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This page was generated on 2022-10-19 13:23:30 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

BUILD results for proFIA on merida1


To the developers/maintainers of the proFIA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proFIA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1500/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proFIA 1.22.0  (landing page)
Alexis Delabriere
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/proFIA
git_branch: RELEASE_3_15
git_last_commit: ecec2db
git_last_commit_date: 2022-04-26 11:37:19 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: proFIA
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data proFIA
StartedAt: 2022-10-18 20:50:38 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:54:25 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 226.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data proFIA
###
##############################################################################
##############################################################################


* checking for file ‘proFIA/DESCRIPTION’ ... OK
* preparing ‘proFIA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘proFIA-vignette.Rmd’ using rmarkdown
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.22.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws


This is xcms version 3.18.0 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

1 directories have been found : mzML

6 files found in directories mzML
 
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C100A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C100B

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C10A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C10B

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C1A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C1B

Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C100A.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C100A

5 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
583 signals detected with an injection between: 17.0-85.2


Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C100B.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C100B

4 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
589 signals detected with an injection between: 17.0-85.5


Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C10A.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C10A

2 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
621 signals detected with an injection between: 17.0-74.7


Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C10B.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C10B

1 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
587 signals detected with an injection between: 14.9-77.9


Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C1A.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C1A

3 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
510 signals detected with an injection between: 14.9-85.3


Create profile matrix with method 'bin' and step 1 ... OK
processing: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/plasFIA/mzML/C1B.mzML

A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection for C1B

4 chromatograms have been used for peak shape determination.
Band filtering: 0 10 20 30 40 50 60 70 80 90 100 
Signal filtering finished.
521 signals detected with an injection between: 17.0-89.5


processus finished 6 samples treated 3411 peaks found.
A mass interval of 0.0307m/z will be used for the density estimation.
0 :0 10 :66 20 :164 30 :243 40 :342 40 :445 50 :540 60 :620 70 :681 80 :722 90 :769 Quitting from lines 214-215 (proFIA-vignette.Rmd) 
Error: processing vignette 'proFIA-vignette.Rmd' failed with diagnostics:
unused argument (plotL = FALSE)
--- failed re-building ‘proFIA-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘proFIA-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted