R CMD check: Sporadic test errors; Error in diff2(x, differences = diff) : names() applied to a non-vector #123
Description
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
...