An error has occurred The application failed to start. signal:killed

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1

The error message from the log is:

2023-05-09T12:34:41.584232+00:00 shinyapps[9065318]: Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31)
2023-05-09T12:34:41.584740+00:00 shinyapps[9065318]: Installing package(s) 'BiocVersion'
2023-05-09T12:34:41.587121+00:00 shinyapps[9065318]: Warning in install.packages(...) :
2023-05-09T12:34:41.587138+00:00 shinyapps[9065318]: 'lib = "/opt/R/4.2.2/lib/R/library"' is not writable
2023-05-09T12:34:41.594467+00:00 shinyapps[9065318]: Error in install.packages(...) : unable to install packages
2023-05-09T12:34:41.594496+00:00 shinyapps[9065318]: Calls: local ... tryCatch -> tryCatchList -> tryCatchOne ->
2023-05-09T12:34:41.594503+00:00 shinyapps[9065318]: Execution halted

Thank you for any fixes or suggestions :smile:

2

You are trying to install a package into a directory /opt/R/4.2.2/lib/R/library where you do not have write access. You can use a function .libPaths() to specify an alternative location with write access.

1 Like
3

Thanks for the response.
No luck with it.

2023-05-15T14:37:25.593138+00:00 shinyapps[9065318]: Bioconductor version '3.16' is out-of-date; the current release version '3.17'
2023-05-15T14:37:25.593185+00:00 shinyapps[9065318]: is available with R version '4.3'; see Bioconductor - Install
2023-05-15T14:37:25.610550+00:00 shinyapps[9065318]: Error in library(BiocVersion, lib.loc = new_lib_path) :
2023-05-15T14:37:25.610593+00:00 shinyapps[9065318]: object 'new_lib_path' not found
2023-05-15T14:37:25.610599+00:00 shinyapps[9065318]: Calls: local ... tryCatch -> tryCatchList -> tryCatchOne ->
2023-05-15T14:37:25.610604+00:00 shinyapps[9065318]: Execution halted
2023-05-15T14:37:25.610609+00:00 shinyapps[9065318]: Shiny application exiting ...

4

This time it is telling you specifically that you have an out of date version of BioConductor. You need to install version 3.17.

5

I overlooked it, and I have fixed it. I installed the latest version and updated R and rstudio.

2023-05-17T08:20:30.235041+00:00 shinyapps[9119680]: Installation paths not writeable, unable to update packages
2023-05-17T08:20:30.235071+00:00 shinyapps[9119680]: path: /opt/R/4.3.0/lib/R/library
2023-05-17T08:20:30.235077+00:00 shinyapps[9119680]: packages:
2023-05-17T08:20:30.235081+00:00 shinyapps[9119680]: class, KernSmooth
2023-05-17T08:20:30.240128+00:00 shinyapps[9119680]: 'getOption("repos")' replaces Bioconductor standard repositories, see
2023-05-17T08:20:30.240155+00:00 shinyapps[9119680]: 'help("repositories", package = "BiocManager")' for details.
2023-05-17T08:20:30.240163+00:00 shinyapps[9119680]: Replacement repositories:
2023-05-17T08:20:30.240178+00:00 shinyapps[9119680]: BioCsoft: Bioconductor - 3.17 Software Packages
2023-05-17T08:20:30.240185+00:00 shinyapps[9119680]: BioCann: Bioconductor - 3.17 AnnotationData Packages
2023-05-17T08:20:30.240192+00:00 shinyapps[9119680]: BioCexp: Bioconductor - 3.17 ExperimentData Packages
2023-05-17T08:20:30.240196+00:00 shinyapps[9119680]: BioCworkflows: Bioconductor - 3.17 Workflow Packages
2023-05-17T08:20:30.241448+00:00 shinyapps[9119680]: BioCbooks: https://bioconductor.org/packages/3.17/books
2023-05-17T08:20:30.241463+00:00 shinyapps[9119680]: CRAN: https://cloud.r-project.org
2023-05-17T08:20:30.920556+00:00 shinyapps[9119680]: Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
2023-05-17T08:20:30.920771+00:00 shinyapps[9119680]: Installing package(s) 'AnnotationDbi'
2023-05-17T08:20:30.923167+00:00 shinyapps[9119680]: Warning in install.packages(...) :
2023-05-17T08:20:30.923176+00:00 shinyapps[9119680]: 'lib = "/opt/R/4.3.0/lib/R/library"' is not writable
2023-05-17T08:20:30.931057+00:00 shinyapps[9119680]: Error in install.packages(...) : unable to install packages
2023-05-17T08:20:30.931073+00:00 shinyapps[9119680]: Calls: local ... tryCatch -> tryCatchList -> tryCatchOne ->
2023-05-17T08:20:30.931078+00:00 shinyapps[9119680]: Execution halted
2023-05-17T08:20:30.931083+00:00 shinyapps[9119680]: Shiny application exiting ...

Another Try
2023-05-17T08:36:42.869286+00:00 shinyapps[9016875]: Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
2023-05-17T08:36:44.315511+00:00 shinyapps[9016875]: Installation paths not writeable, unable to update packages
2023-05-17T08:36:44.315564+00:00 shinyapps[9016875]: path: /opt/R/4.3.0/lib/R/library
2023-05-17T08:36:44.315572+00:00 shinyapps[9016875]: packages:
2023-05-17T08:36:44.315576+00:00 shinyapps[9016875]: class, KernSmooth
2023-05-17T08:36:45.064207+00:00 shinyapps[9016875]: Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
2023-05-17T08:36:45.064696+00:00 shinyapps[9016875]: Warning: package(s) not installed when version(s) same as or greater than current; use
2023-05-17T08:36:45.064715+00:00 shinyapps[9016875]: force = TRUE to re-install: 'BiocVersion'
2023-05-17T08:36:45.065003+00:00 shinyapps[9016875]: Installing package(s) 'AnnotationDbi'
2023-05-17T08:36:45.067619+00:00 shinyapps[9016875]: Warning in install.packages(...) :
2023-05-17T08:36:45.067650+00:00 shinyapps[9016875]: 'lib = "/opt/R/4.3.0/lib/R/library"' is not writable
2023-05-17T08:36:45.076064+00:00 shinyapps[9016875]: Error in install.packages(...) : unable to install packages
2023-05-17T08:36:45.076112+00:00 shinyapps[9016875]: Calls: local ... tryCatch -> tryCatchList -> tryCatchOne ->
2023-05-17T08:36:45.076117+00:00 shinyapps[9016875]: Execution halted
2023-05-17T08:36:45.076120+00:00 shinyapps[9016875]: Shiny application exiting ...

'lib = "/opt/R/4.3.0/lib/R/library"' is not writable
I am working on windows, /opt looks like it would for Linux.

6

This is why you need to set your own library path, for example

.libPaths("here-path-to-your-directory")
7

Thank you very much for your help. The error is resolved.
I removed the biocmanager::install call explicitly.

8

2023-05-17T11:24:17.133383+00:00 shinyapps[9127426]: Attaching package: ‘IRanges’
2023-05-17T11:24:17.133553+00:00 shinyapps[9127426]: The following object is masked from ‘package:lubridate’:
2023-05-17T11:24:17.133592+00:00 shinyapps[9127426]: %within%
2023-05-17T11:24:17.133755+00:00 shinyapps[9127426]: The following object is masked from ‘package:purrr’:
2023-05-17T11:24:17.133771+00:00 shinyapps[9127426]: reduce
2023-05-17T11:24:17.133956+00:00 shinyapps[9127426]: The following objects are masked from ‘package:dplyr’:
2023-05-17T11:24:17.133969+00:00 shinyapps[9127426]: collapse, desc, slice
2023-05-17T11:24:17.135049+00:00 shinyapps[9127426]: Loading required package: GenomicRanges
2023-05-17T11:24:17.139125+00:00 shinyapps[9127426]: Loading required package: GenomeInfoDb
2023-05-17T11:24:17.964351+00:00 shinyapps[9127426]: Loading required package: SummarizedExperiment
2023-05-17T11:24:17.966360+00:00 shinyapps[9127426]: Loading required package: MatrixGenerics
2023-05-17T11:24:17.967929+00:00 shinyapps[9127426]: Loading required package: matrixStats
2023-05-17T11:24:17.979814+00:00 shinyapps[9127426]: Attaching package: ‘matrixStats’
2023-05-17T11:24:17.980023+00:00 shinyapps[9127426]: The following object is masked from ‘package:dplyr’:
2023-05-17T11:24:17.980048+00:00 shinyapps[9127426]: count
2023-05-17T11:24:18.083520+00:00 shinyapps[9127426]: Attaching package: ‘MatrixGenerics’
2023-05-17T11:24:18.084091+00:00 shinyapps[9127426]: The following objects are masked from ‘package:matrixStats’:
2023-05-17T11:24:18.084125+00:00 shinyapps[9127426]: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2023-05-17T11:24:18.084130+00:00 shinyapps[9127426]: colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2023-05-17T11:24:18.084149+00:00 shinyapps[9127426]: colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2023-05-17T11:24:18.084178+00:00 shinyapps[9127426]: colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2023-05-17T11:24:18.084188+00:00 shinyapps[9127426]: colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2023-05-17T11:24:18.084193+00:00 shinyapps[9127426]: colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2023-05-17T11:24:18.084198+00:00 shinyapps[9127426]: colWeightedMeans, colWeightedMedians, colWeightedSds,
2023-05-17T11:24:18.084204+00:00 shinyapps[9127426]: colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2023-05-17T11:24:18.084209+00:00 shinyapps[9127426]: rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2023-05-17T11:24:18.084233+00:00 shinyapps[9127426]: rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2023-05-17T11:24:18.084247+00:00 shinyapps[9127426]: rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2023-05-17T11:24:18.084252+00:00 shinyapps[9127426]: rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2023-05-17T11:24:18.084256+00:00 shinyapps[9127426]: rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2023-05-17T11:24:18.084289+00:00 shinyapps[9127426]: rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2023-05-17T11:24:18.084297+00:00 shinyapps[9127426]: rowWeightedSds, rowWeightedVars
2023-05-17T11:24:18.111191+00:00 shinyapps[9127426]: Loading required package: Biobase
2023-05-17T11:24:18.332280+00:00 shinyapps[9127426]: Welcome to Bioconductor
2023-05-17T11:24:18.332327+00:00 shinyapps[9127426]: Vignettes contain introductory material; view with
2023-05-17T11:24:18.332331+00:00 shinyapps[9127426]: 'browseVignettes()'. To cite Bioconductor, see
2023-05-17T11:24:18.332334+00:00 shinyapps[9127426]: 'citation("Biobase")', and for packages 'citation("pkgname")'.
2023-05-17T11:24:18.337091+00:00 shinyapps[9127426]: Attaching package: ‘Biobase’
2023-05-17T11:24:18.337355+00:00 shinyapps[9127426]: The following object is masked from ‘package:MatrixGenerics’:
2023-05-17T11:24:18.337380+00:00 shinyapps[9127426]: rowMedians
2023-05-17T11:24:18.337563+00:00 shinyapps[9127426]: The following objects are masked from ‘package:matrixStats’:
2023-05-17T11:24:18.337584+00:00 shinyapps[9127426]: anyMissing, rowMedians
2023-05-17T11:24:22.652199+00:00 shinyapps[9127426]: Attaching package: ‘glue’
2023-05-17T11:24:22.652354+00:00 shinyapps[9127426]: The following object is masked from ‘package:SummarizedExperiment’:
2023-05-17T11:24:22.652395+00:00 shinyapps[9127426]: trim
2023-05-17T11:24:22.652560+00:00 shinyapps[9127426]: The following object is masked from ‘package:GenomicRanges’:
2023-05-17T11:24:22.652582+00:00 shinyapps[9127426]: trim
2023-05-17T11:24:22.652720+00:00 shinyapps[9127426]: The following object is masked from ‘package:IRanges’:
2023-05-17T11:24:22.652737+00:00 shinyapps[9127426]: trim
2023-05-17T11:24:42.531176+00:00 shinyapps[9127426]: Container event from container-8151684: oom (out of memory)

Any work arounds will be helpful.