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 g...@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.b...@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 g...@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-boun...@r-project.org on behalf of tiago.lubiana.al...@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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> Bioc-devel@r-project.org mailing list
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>
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