sneumann
commented
3 years ago The most informative error I see locally is
Beginning band detection for C100B
4 chromatograms have been used for peak shape determination.
Error in determiningInjectionZoneFromTIC(list(intensity = nTIC, scan = seq_along(nTIC)), :
trying to get slot "scantime" from an object of a basic class ("list") with no slots
Calls: findFIASignal ... getInjectionPeak -> determiningInjectionZoneFromTIC
Execution haltedFull output of a local R CMD check
R CMD check proFIA
* using log directory ‘/vol/R/BioC/devel/proFIA.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘proFIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proFIA’ version ‘1.15.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘proFIA/src’ contains apparent object files/libraries
FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o proFIA.so
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.gitignore
.git
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘proFIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* 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 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
persoConv: no visible global function definition for ‘dexp’
Undefined global functions or variables:
dexp
Consider adding
importFrom("stats", "dexp")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimateNoiseMS':
estimateNoiseMS
Code: function(list_files, ppm, nBin = 500, minInt = 500, maxInt =
10^8, f = c("TIC", "regression"), parallel,
includeZero = TRUE, dmz = 5e-04, BPPARAM = NULL)
Docs: function(list_files, ppm, nBin = 500, minInt = 500, maxInt =
10^8, parallel, includeZero = TRUE, dmz = 5e-04,
BPPARAM = NULL)
Argument names in code not in docs:
f
Mismatches in argument names (first 3):
Position: 6 Code: f Docs: parallel
Position: 7 Code: parallel Docs: includeZero
Position: 8 Code: includeZero Docs: dmz
Codoc mismatches from documentation object 'proFIAset':
proFIAset
Code: function(path, ppm, parallel = TRUE, BPPARAM = NULL,
noiseEstimation = TRUE, f = c("regression", "TIC"),
graphical = FALSE, ...)
Docs: function(path, ppm, parallel = TRUE, BPPARAM = NULL,
noiseEstimation = TRUE, graphical = FALSE, ...)
Argument names in code not in docs:
f
Mismatches in argument names:
Position: 6 Code: f Docs: graphical
Position: 7 Code: graphical Docs: ...
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'findFIASignal'
‘shiftFactor’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘group_good_parameters.png’, ‘group_wrong_parameters.png’,
‘proFIA-vignette.Rmd’, ‘proFIA-vignette.bib’,
‘proFIA_cheat_sheet.png’, ‘workflow_info.png’
* checking examples ... ERROR
Running examples in ‘proFIA-Ex.R’ failed
The error most likely occurred in:
> ### Name: findFIASignal
> ### Title: Detect peaks in an FIA acquisition.
> ### Aliases: findFIASignal findPeaks
>
> ### ** Examples
>
> if(require(plasFIA)){
+ #Getting the path of a file.
+ path_raw<-list.files(system.file(package="plasFIA","mzML"),full.names=TRUE)[2]
+
+ #Opening the file with xcms
+ xraw<-xcmsRaw(path_raw)
+
+ ppm<-2
+
+ #getting the filtered signals without noise model which is not recommended.
+ tsignal<-findFIASignal(xraw,ppm=ppm,SNT=3)
+
+ #Getting the noise model un the plasSet object.
+ data(plasSet)
+ es<-attr(plasSet,"noiseEstimation")
+
+ #Getting the signal with a noise model.
+ tsignal<-findFIASignal(xraw,ppm=2,es=es,pvalthresh=0.005)
+ head(tsignal)
+ }
Loading required package: plasFIA
Create profile matrix with method 'bin' and step 1 ... OK
No noise model provided, a signal/solvant threshold will be used.
Beginning band detection for C100B
4 chromatograms have been used for peak shape determination.
Error in determiningInjectionZoneFromTIC(list(intensity = nTIC, scan = seq_along(nTIC)), :
trying to get slot "scantime" from an object of a basic class ("list") with no slots
Calls: findFIASignal ... getInjectionPeak -> determiningInjectionZoneFromTIC
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
dir.exists(dir) is not TRUE
Package vignette without corresponding single PDF/HTML:
‘proFIA-vignette.Rmd’
* checking running R code from vignettes ...
‘proFIA-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
--- re-building ‘proFIA-vignette.Rmd’ using rmarkdown
Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.15.4
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 3.11.5
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: /usr/local/lib/R/site-library/plasFIA/mzML/C100A.mzML
Quitting from lines 94-99 (proFIA-vignette.Rmd)
Error: processing vignette 'proFIA-vignette.Rmd' failed with diagnostics:
argument "f" is missing, with no default
--- failed re-building ‘proFIA-vignette.Rmd’
SUMMARY: processing the following file failed:
‘proFIA-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 6 WARNINGs, 3 NOTEs
See
‘/vol/R/BioC/devel/proFIA.Rcheck/00check.log’
for details.
Hi, currently proFIA fails on BioC with an ERROR:
http://bioconductor.org/checkResults/devel/bioc-LATEST/proFIA/malbec1-buildsrc.html
Unfortunately the error message is not very descriptive:
Yours, Steffen