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An error regarding a jpeg call in the server #10

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Fight-a-tiger-in-the-mountain opened this issue Nov 27, 2023 · 0 comments
Open

An error regarding a jpeg call in the server #10

Fight-a-tiger-in-the-mountain opened this issue Nov 27, 2023 · 0 comments

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@Fight-a-tiger-in-the-mountain

Hello, I have been having trouble getting around the jpeg device call when doing calculations with your REMBRANDTS (the server does not display the device) and reporting an error: “Error in jpeg(file = paste(outputFolder, "/vsd_normalized.", readType, : unable to start device 'jpeg'In addition: Warning message: In jpeg(file = paste(outputFolder, "/vsd_normalized.", readType, : cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, et>Execution halted”

The details are as follows:
input command:
bash ./REMBRANDTS.sh mRNA_stability metadata.list / 0.99 linear

Complete error log:
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

findMatches

The following objects are masked from ‘package:base’:

expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: Biobase
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

Attaching package: ‘gplots’

The following object is masked from ‘package:IRanges’:

space

The following object is masked from ‘package:S4Vectors’:

space

The following object is masked from ‘package:stats’:

lowess

Error in jpeg(file = paste(outputFolder, "/vsd_normalized.", readType, :
unable to start device 'jpeg'
In addition: Warning message:
In jpeg(file = paste(outputFolder, "/vsd_normalized.", readType, :
cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Execution halted

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file './tmp/mRNA_stability/vsd_normalized.intronic.all.centered.mx.txt': No such file or directory
Execution halted

Hope to get your help, thank you

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