[Bioc-devel] Build failing for package 'fcoex' and I do not know why

[Tiago Lubiana]

Hello, Martin,

Thank you very much for your reply and sorry about the delay.

I have removed the cached files from the repository and added them to
.gitignore.

I was not running the most updated version of BiocManager, and not using
R-devel (my fault, I'm sorry)

As you did, now I did:

BiocManager::version()  # 3.13, the current release
BiocManager::valid()    # TRUE, all packages are up-to-date
BiocManager::install("fcoex")  # a short-cut to install dependencies

cd /tmp
 git clone --depth 1 git using git.bioconductor.org:packages/fcoex
R CMD build fcoex

I get the same mistake as you do now.

I am working to find out the errors and make a fix, and I'll try the docker
image too, thank you for the reminder.
Once again, I am sorry for the problems,
Best regards,

Tiago




On Thu, Dec 24, 2020 at 5:34 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> Actually, I generate other errors, but not the build report errors.
>
> I see your package git repository includes 'cached' files,
> vignettes/fcoex_files; these are not appropriate for a git repository,
> since they reflect some state on your particular machine, rather than on
> the build system or user machines in general.
>
> Here's what I did:
>
>   BiocManager::version()  # 3.13, the current release
>   BiocManager::valid()    # TRUE, all packages are up-to-date
>   BiocManager::install("fcoex")  # a short-cut to install dependencies
>
> Then I tried to build your package, making sure I had no weird files or
> uncomitted changes
>
>   cd /tmp
>   git clone --depth 1 git using git.bioconductor.org:packages/fcoex
>   R CMD build fcoex
>
> The output was
>
> * checking for file 'fcoex/DESCRIPTION' ... OK
> * preparing 'fcoex':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘fcoex.Rmd’ using rmarkdown
>
>
> Attaching package: 'MatrixGenerics'
>
> The following objects are masked from 'package:matrixStats':
>
>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
>     colWeightedMeans, colWeightedMedians, colWeightedSds,
>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
>     rowWeightedSds, rowWeightedVars
>
>
> 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.max, which.min
>
>
> Attaching package: 'S4Vectors'
>
> The following objects are masked from 'package:base':
>
>     I, expand.grid, unname
>
> Welcome to Bioconductor
>
>     Vignettes contain introductory material; view with
>     'browseVignettes()'. To cite Bioconductor, see
>     'citation("Biobase")', and for packages 'citation("pkgname")'.
>
>
> Attaching package: 'Biobase'
>
> The following object is masked from 'package:MatrixGenerics':
>
>     rowMedians
>
> The following objects are masked from 'package:matrixStats':
>
>     anyMissing, rowMedians
>
> Created new fcoex object.
> Getting SU scores
> Running FCBF to find module headers
> Calculating adjacency matrix
> Trimming and getting modules from adjacency matrix
> Warning in file(con, "rb") :
>   file("") only supports open = "w+" and open = "w+b": using the former
> Warning in readChar(file, nchars = nChars, useBytes = TRUE) :
>   text connection used with readChar(), results may be incorrect
> Quitting from lines 117-122 (fcoex.Rmd)
> Error: processing vignette 'fcoex.Rmd' failed with diagnostics:
> invalid 'nchars' argument
> --- failed re-building ‘fcoex.Rmd’
>
> SUMMARY: processing the following file failed:
>   ‘fcoex.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> I know that this is a different error from on the build system, but it
> points to some problems. What do you see? Have you tried to reproduce the
> problem reported on the build system using the docker image described at
> http://bioconductor.org/help/docker/ ?
>
> Martin
>
> On 12/24/20, 2:58 PM, "Bioc-devel on behalf of Tiago Lubiana" <
> bioc-devel-bounces using r-project.org on behalf of tiago.lubiana.alves using usp.br>
> wrote:
>
>     Hello all,
>
>     One package that I manage is failing both Devel and Release:
>     Devel:
>     bioconductor.org/checkResults/devel/bioc-LATEST/fcoex
>
>     Release:
>     bioconductor.org/checkResults/release/bioc-LATEST/fcoex
>
>     A part code generates some plots and then saves them to a folder. This
> is
>     failing in all machines, but I cannot reproduce the error on my
> computer
>     (Ubuntu 18.04).
>
>       save_plots(fc, name = "Example")
>
>     Saving available plots.
>     $TYROBP
>     Error in `$<-.data.frame`(`*tmp*`, "point.size", value = numeric(0)) :
>       replacement has 0 rows, data has 10
>     Calls: save_plots ... makeContent.labelrepeltree -> $<- ->
> $<-.data.frame
>     Execution halted
>
>     Does anyone know what might be happening?
>
>     Thank you very much and have happy (and safe) celebrations :)
>
>     Best,
>     Tiago
>
>
>     *------------------------------------*
>     *Tiago Lubiana *
>     *PhD Candidate in Bioinformatics, University of São Paulo*
>     *Computational Systems Biology Laboratory (CSBL)*
>
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>
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