R CMD check: Sporadic test errors; Error in diff2(x, differences = diff) : names() applied to a non-vector

[HenrikBengtsson]

When running reverse package depdencies checks, QDNAseq sometimes gives the following error:

* using R version 4.3.2 (2023-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)
    GNU Fortran (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)
* running under: CentOS Linux 7 (Core)
...
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... ERROR
  Running ‘QDNAseq,copyneutral.R’
  Running ‘QDNAseq,gain-copyneutral-gain.R’
  Running ‘QDNAseq,parallel-reproducibility.R’
  Running ‘QDNAseq.R’
Running the tests in ‘tests/QDNAseq.R’ failed.
Last 50 lines of output:
  EM algorithm done ...
  
  Computing posterior probabilities for all segments ...
  
  Total time:0minutes
  
  Adjusting segmented data for cellularity ... 
  
  Cellularity sample1: 1
  
  1
  40166888406795214.664.2784080416214037418.8123.8784080413445031418.8102.6
  40167078573541214.665.5784080416214037418.8123.8784080413445031418.8102.6
  40167048573535214.665.5784080416214037418.8123.8784080413445031418.8102.6
  40167328840550214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40171598841505214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40171688841509214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40171778841513214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40171868841517214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40171958841521214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40172018841524214.667.5784080416214037418.8123.8784080413445031418.8102.6
  40172208908254214.668784080416214037418.8123.8784080413445031418.8102.6
  40176378908577214.668784080416214037418.8123.8784080413445031418.8102.6
  FINISHED!
  
  Total time:0minutes
  
  There were 50 or more warnings (use warnings() to see the first 50)
  > print(fitC)
  QDNAseqCopyNumbers (storageMode: lockedEnvironment)
  assayData: 38819 features, 1 samples 
    element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented 
  protocolData: none
  phenoData
    sampleNames: LGG150
    varLabels: name reads ... loess.family (6 total)
    varMetadata: labelDescription
  featureData
    featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
      (38819 total)
    fvarLabels: chromosome start ... use (9 total)
    fvarMetadata: labelDescription
  experimentData: use 'experimentData(object)'
  Total time:0minutes
  
  There were 50 or more warnings (use warnings() to see the first 50)
  > print(fitC)
  QDNAseqCopyNumbers (storageMode: lockedEnvironment)
  assayData: 38819 features, 1 samples 
    element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented 
  protocolData: none
  phenoData
    sampleNames: LGG150
    varLabels: name reads ... loess.family (6 total)
    varMetadata: labelDescription
  featureData
    featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
      (38819 total)
    fvarLabels: chromosome start ... use (9 total)
    fvarMetadata: labelDescription
  experimentData: use 'experimentData(object)'
  Annotation:  
  > plot(fitC)
  Error in diff2(x, differences = diff) : names() applied to a non-vector
  Calls: plot -> plot -> .local -> apply -> FUN -> sdDiff -> diff2
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘QDNAseq.Rnw’... OK
* checking re-building of vignette outputs ... NOTE
...

[HenrikBengtsson]

In yet another revdep run, I got:

  experimentData: use 'experimentData(object)'
  Annotation:  
  > plot(fitC)
  
   *** caught segfault ***
  address (nil), cause 'unknown'
  
  Traceback:
   1: diff2(x, differences = diff)
   2: sdDiff(x, ..., trim = trim)
   3: FUN(newX[, i], ...)
   4: apply(copynumber, MARGIN = 2L, FUN = sdFUN, na.rm = TRUE)
   5: .local(x, y = y, ...)
   6: plot(fitC)
   7: plot(fitC)
  An irrecoverable exception occurred. R is aborting now ...

[SQ-Gao]

I encountered a similar situation. Have you resolved it?

[HenrikBengtsson]

I encountered a similar situation. Have you resolved it?

Which? There are two mentioned in above comments.

As far as I know, there has been no attempts to track this down or to fix either of them.