Question: Error: C stack usage when installing Txdb package
0
gravatar for Mark Dunning
21 months ago by
Mark Dunning1.1k
Sheffield, Uk
Mark Dunning1.1k wrote:

Hi all,

I'm trying to install the TxDb.Hsapiens.UCSC.hg38.knownGene package, but getting pretty stumped at an error to do with C stack usage.

 

source("http://www.bioconductor.org/biocLite.R")

biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")

 

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).

Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz'

Content type 'application/x-gzip' length 31934087 bytes (30.5 MB)

==================================================

downloaded 30.5 MB


* installing *source* package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ ...

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

Error: package or namespace load failed for ‘TxDb.Hsapiens.UCSC.hg38.knownGene’:

 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg38.knownGene', details:

  call: NULL

  error: C stack usage  7969316 is too close to the limit

Error: loading failed

Execution halted

ERROR: loading failed

* removing ‘/home/dunnin01/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg38.knownGene’


The downloaded source packages are in

‘/tmp/RtmpkCKEiJ/downloaded_packages’

installation path not writeable, unable to update packages: boot, class,

 

Can anyone suggest how I might fix this? Here is my session info. Many thanks,

 

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2   
ADD COMMENTlink modified 21 months ago by Simon Anders3.6k • written 21 months ago by Mark Dunning1.1k

Same problem here:

Error: package or namespace load failed for ‘TxDb.Hsapiens.UCSC.hg19.knownGene’:
 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: NULL
  error: C stack usage  7969716 is too close to the limit

I tried Martin's suggestion  to install without test; now the error occurs when I try to load the package.

 

Session Info

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2        
[4] GenomicRanges_1.28.6   GenomeInfoDb_1.12.3    IRanges_2.10.5        
[7] S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               XVector_0.16.0            
 [3] GenomicAlignments_1.12.2   zlibbioc_1.22.0           
 [5] BiocParallel_1.10.1        bit_1.1-12                
 [7] lattice_0.20-33            rlang_0.1.4               
 [9] blob_1.1.0                 tools_3.4.2               
[11] grid_3.4.2                 SummarizedExperiment_1.6.5
[13] DBI_0.7                    matrixStats_0.52.2        
[15] bit64_0.9-7                digest_0.6.12             
[17] tibble_1.3.4               Matrix_1.2-3              
[19] GenomeInfoDbData_0.99.0    rtracklayer_1.36.6        
[21] bitops_1.0-6               RCurl_1.95-4.8            
[23] biomaRt_2.32.1             memoise_1.1.0             
[25] RSQLite_2.0                DelayedArray_0.2.7        
[27] compiler_3.4.2             Rsamtools_1.28.0          
[29] Biostrings_2.44.2          XML_3.98-1.9              
> 

 

ADD REPLYlink written 21 months ago by Simon Anders3.6k

I have debugged it a bit and it seems the error is triggered by .onLoad in zzz.R

I can trigger it manually with 

> AnnotationDbi::loadDb( "~/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" )
Error: C stack usage  7970340 is too close to the limit

Note: The error appears when I execute the command the second time. Observe:

anders@merlot:~$ R

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> AnnotationDbi::loadDb( "~/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" )
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

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’:

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.

Error in AnnotationDbi:::.getMetaValue(dbconn(txdb), "DBSCHEMAVERSION") :
  invalid DB file
> AnnotationDbi::loadDb( "~/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" )
Error: C stack usage  7970340 is too close to the limit
> 

Could it be that the sqlite file in the repo got corrupted?

ADD REPLYlink modified 21 months ago • written 21 months ago by Simon Anders3.6k
On Tue, Dec 12, 2017 at 12:54 PM, Simon Anders [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Simon Anders <https: support.bioconductor.org="" u="" 3855=""/> wrote Comment: > Error: C stack usage when installing Txdb package > <https: support.bioconductor.org="" p="" 103995="" #104064="">: > > I have debugged it a bit and it seems the error is triggered by .onLoad in > zzz.R > > I can trigger it manually with > > > AnnotationDbi::loadDb( "~/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" ) > Error: C stack usage 7970340 is too close to the limit > > *Note: *The error appears when I execute the command the second time. > Observe: > > anders@merlot:~$ R > > R version 3.4.2 (2017-09-28) -- "Short Summer" > Copyright (C) 2017 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > AnnotationDbi::*loadDb*( "~/R/x86_64-pc-linux-gnu- > library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/ > TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" ) > Loading required package: GenomicFeatures > Loading required package: BiocGenerics > Loading required package: parallel > > 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’: > > anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, > colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, > grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, > mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which, which.max, which.min > > Loading required package: S4Vectors > Loading required package: stats4 > > Attaching package: ‘S4Vectors’ > > The following object is masked from ‘package:base’: > > expand.grid > > Loading required package: IRanges > Loading required package: GenomeInfoDb > Loading required package: GenomicRanges > Loading required package: AnnotationDbi > 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")'. > > > *Error in AnnotationDbi:::.getMetaValue(dbconn(txdb), "DBSCHEMAVERSION") : > invalid DB file* > > AnnotationDbi::*loadDb*( "~/R/x86_64-pc-linux-gnu- > library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene/extdata/ > TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" ) > *Error: C stack usage 7970340 is too close to the limit* > > > > Could it be that the sqlite file in the repo got corrupted? > Maybe if you got it from a different mirror. But the one at bioconductor.org seems OK jmacdon@ogopogo:~$ wget http://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz --2017-12-12 11:11:17-- http://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz Resolving bioconductor.org bioconductor.org)... 13.33.151.6, 13.33.151.236, 13.33.151.78, ... Connecting to bioconductor.org bioconductor.org)|13.33.151.6|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 18669702 (18M) [application/x-gzip] Saving to: ‘TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz’ TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz 100%[==========================================================================================================================================>] 17.80M 16.6MB/s in 1.1s 2017-12-12 11:11:18 (16.6 MB/s) - ‘TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz’ saved [18669702/18669702] jmacdon@ogopogo:~$ tar xvfz TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz Then from within R > library(AnnotationDbi) > library(DBI) > con <- dbConnect(SQLite(), "TxDb.Hsapiens.UCSC.hg19.knownGene/inst/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite") !> AnnotationDbi:::.getMetaValue(con, "DBSCHEMAVERSION") [1] "1.1" ------------------------------ > > Post tags: txdb.hsapiens.ucsc.hg38.knowngene, org.hs.eg.db > > You may reply via email or visit https://support.bioconductor. > org/p/103995/#104064 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 21 months ago by James W. MacDonald51k

It's not the sqlite file. I've dug a bit deeper. Evidence points to the GenomicFeatures package.

See here:

I start with a fresh R session

anders@merlot:~$ R
R version 3.4.2 (2017-09-28) -- "Short Summer"

I connect to the sqlite file:

> conn <- AnnotationDbi::dbFileConnect( "tmp/TxDb.Hsapiens.UCSC.hg19.knownGene/inst/extdata/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite" )

Now, I load all packages that GenomicFeature depends on

> library(GenomicRanges)
> library(AnnotationDbi)
> library(Biobase)
[output omitted]

I check something in the database. This still works:

> RSQLite::dbExistsTable( conn, "metadata" )
[1] TRUE
​

Now I load GenomicFeatures, and then, the same command suddenly fails:

> library(GenomicFeatures)
> RSQLite::dbExistsTable( conn, "metadata" )
Error: C stack usage  7969492 is too close to the limit
ADD REPLYlink written 21 months ago by Simon Anders3.6k

Does BiocInstaller::biocValid() provide any insight? Mark's download of TxDb... v. 3.4.0 from Bioc v. 3.6 is not consistent with most of your package versions (from Bioc v.3.5., e.g., GenomicFeatures 1.28.5 versus 1.30.0).

ADD REPLYlink written 21 months ago by Martin Morgan ♦♦ 23k
>  BiocInstaller::biocValid()
[1] TRUE
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2        
[4] GenomicRanges_1.28.6   GenomeInfoDb_1.12.3    IRanges_2.10.5        
[7] S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               BiocInstaller_1.26.1      
 [3] compiler_3.4.2             XVector_0.16.0            
 [5] bitops_1.0-6               tools_3.4.2               
 [7] zlibbioc_1.22.0            biomaRt_2.32.1            
 [9] digest_0.6.12              bit_1.1-12                
[11] lattice_0.20-33            RSQLite_2.0               
[13] memoise_1.1.0              tibble_1.3.4              
[15] pkgconfig_2.0.1            rlang_0.1.4               
[17] Matrix_1.2-3               DelayedArray_0.2.7        
[19] DBI_0.7                    GenomeInfoDbData_0.99.0   
[21] rtracklayer_1.36.6         Biostrings_2.44.2         
[23] bit64_0.9-7                grid_3.4.2                
[25] XML_3.98-1.9               BiocParallel_1.10.1       
[27] blob_1.1.0                 Rsamtools_1.28.0          
[29] matrixStats_0.52.2         GenomicAlignments_1.12.2  
[31] SummarizedExperiment_1.6.5 RCurl_1.95-4.8            
ADD REPLYlink written 21 months ago by Simon Anders3.6k

And the version of the TxDb package you're trying to load (maybe packageVersion("TxDb...") would work?). Also, at the end of the day, it'll be at least an 'update your Bioconductor installation' response, since we can't update Bioc 3.5 packages.

ADD REPLYlink modified 21 months ago • written 21 months ago by Martin Morgan ♦♦ 23k

I've just noticed that I had not yet updated to the newest Bioc release, so I just did a BiocUpgrade. However, the error persists. Also, the issue happens with other db packages, too.

For example:

If I run, in a fresh R session, "library( org.Hs.db.eg )", and then, "library( GenomicFeatures )", this works.

If, however, again in a fresh R session, i first issue "library( GenomicFeatures )", and then "library( org.Hs.db.eg )", this fails with the C stack error.

So, it depends on the order in which the packages are loaded. It seems that GenomicFeatures has to be loaded after any annotation database package. This, however, does not work for TxDb packages, because they depend on GenomicFeatures and so load that first.

This is now with GenomicFeatures 1.30.0.

Full session info:

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.30.0 GenomicRanges_1.30.0   GenomeInfoDb_1.14.0   
[4] org.Hs.eg.db_3.5.0     AnnotationDbi_1.40.0   IRanges_2.12.0        
[7] S4Vectors_0.16.0       Biobase_2.38.0         BiocGenerics_0.24.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               compiler_3.4.2            
 [3] XVector_0.18.0             prettyunits_1.0.2         
 [5] bitops_1.0-6               tools_3.4.2               
 [7] zlibbioc_1.24.0            progress_1.1.2            
 [9] biomaRt_2.34.0             digest_0.6.12             
[11] bit_1.1-12                 lattice_0.20-33           
[13] RSQLite_2.0                memoise_1.1.0             
[15] tibble_1.3.4               pkgconfig_2.0.1           
[17] rlang_0.1.4                Matrix_1.2-3              
[19] DelayedArray_0.4.1         DBI_0.7                   
[21] GenomeInfoDbData_0.99.1    rtracklayer_1.38.2        
[23] stringr_1.2.0              Biostrings_2.46.0         
[25] grid_3.4.2                 bit64_0.9-7               
[27] R6_2.2.2                   BiocParallel_1.12.0       
[29] XML_3.98-1.9               RMySQL_0.10.13            
[31] blob_1.1.0                 magrittr_1.5              
[33] matrixStats_0.52.2         GenomicAlignments_1.14.1  
[35] Rsamtools_1.30.0           SummarizedExperiment_1.8.0
[37] assertthat_0.2.0           stringi_1.1.6             
[39] RCurl_1.95-4.8            


 
ADD REPLYlink written 21 months ago by Simon Anders3.6k

I managed to rid my system of the error. I had noticed that it has nothing to do with the annotation packages at all, because S4 as a whole was broken: The "C stack limit" error happened whenever I called any S4 method after loading GenomicFeatures. So, I updated all those base installation packages that biocUpgrade and update.packages usually skip because the system library directory is not writable. Not sure which of them it was but that did it; now everything works.

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.30.0                 
[3] AnnotationDbi_1.40.0                    GenomicRanges_1.30.0                   
[5] GenomeInfoDb_1.14.0                     IRanges_2.12.0                         
[7] S4Vectors_0.16.0                        Biobase_2.38.0                         
[9] BiocGenerics_0.24.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               compiler_3.4.2             XVector_0.18.0             prettyunits_1.0.2         
 [5] bitops_1.0-6               tools_3.4.2                zlibbioc_1.24.0            progress_1.1.2            
 [9] biomaRt_2.34.0             digest_0.6.12              bit_1.1-12                 lattice_0.20-35           
[13] RSQLite_2.0                memoise_1.1.0              tibble_1.3.4               pkgconfig_2.0.1           
[17] rlang_0.1.4                Matrix_1.2-12              DelayedArray_0.4.1         DBI_0.7                   
[21] yaml_2.1.15                GenomeInfoDbData_0.99.1    rtracklayer_1.38.2         stringr_1.2.0             
[25] Biostrings_2.46.0          grid_3.4.2                 bit64_0.9-7                R6_2.2.2                  
[29] XML_3.98-1.9               RMySQL_0.10.13             BiocParallel_1.12.0        blob_1.1.0                
[33] magrittr_1.5               matrixStats_0.52.2         Rsamtools_1.30.0           GenomicAlignments_1.14.1  
[37] SummarizedExperiment_1.8.0 assertthat_0.2.0           stringi_1.1.6              RCurl_1.95-4.8      

 

ADD REPLYlink written 21 months ago by Simon Anders3.6k
Answer: Error: C stack usage when installing Txdb package
1
gravatar for Simon Anders
21 months ago by
Simon Anders3.6k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.6k wrote:

On my system, updating the base packages solved the issue. (See: https://support.bioconductor.org/p/103995/#104087)

ADD COMMENTlink written 21 months ago by Simon Anders3.6k

I am having the same problem working on my server. To clarify you had to update the base R packages? Or updated dependencies of GenomicFeatures? Thank you!

ADD REPLYlink written 7 months ago by amaggio0
Answer: Error: C stack usage when installing Txdb package
0
gravatar for Martin Morgan
21 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

My guess is that it is some dependency that is failing, rather than the package itself. You could install the package first

biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene", INSTALL_opts="--no-test-load")

and then load it

library("TxDb.Hsapiens.UCSC.hg38.knownGene")

for perhaps more revelation? If it continues to fail, you might try BiocInstaller::biocValid() to check for version incompatibilities.

ADD COMMENTlink modified 21 months ago • written 21 months ago by Martin Morgan ♦♦ 23k
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