Updating packages, Bioconductor 3.5: "package or namespace load failed for GO.db"
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gctromp ▴ 10
@gctromp-7356
Last seen 4.2 years ago
United States

I upgraded to R 3.4.1 yesterday and ran biocLite to update the biocInstaller and bioconductor packages.

A number of packages that depend on GO.db are failing to install with the following error: package or namespace load failed for ‘GO.db’

Additional error message fall into two categories:

  1. call: NULL
      error: C stack usage  7970996 is too close to the limit
  2.   call: NULL
      error: evaluation nested too deeply: infinite recursion / options(expressions=)?

Strangely, GO.db loads fine in an interactive session.

Increasing  the stack limit (ulimit) for the shell session does not change the behavior.

I saw a suggestion to try biocLite(c("AnnotationDbi", "GO.db"), type="source")

and did that (even though *source* is always used on Linux), and it did not solve the problem.

Does anyone have a suggestion?

Gerard

 


SessionInfo for "R --vanilla

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 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_ZA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_ZA.UTF-8        LC_COLLATE=en_ZA.UTF-8    
 [5] LC_MONETARY=en_ZA.UTF-8    LC_MESSAGES=en_ZA.UTF-8   
 [7] LC_PAPER=en_ZA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C       
                                                                                                                                                                                                      
attached base packages:                                                                                                                                                                               
[1] stats     graphics  grDevices utils     datasets  methods   base                                                                                                                                  
                                                                                                                                                                                                      
loaded via a namespace (and not attached):                                                                                                                                                            
[1] compiler_3.4.1                                

 


And with GO.db loaded:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 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_ZA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_ZA.UTF-8        LC_COLLATE=en_ZA.UTF-8    
 [5] LC_MONETARY=en_ZA.UTF-8    LC_MESSAGES=en_ZA.UTF-8   
 [7] LC_PAPER=en_ZA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GO.db_3.4.1          AnnotationDbi_1.38.2 IRanges_2.10.2      
[4] S4Vectors_0.14.3     Biobase_2.36.2       BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12    digest_0.6.12   DBI_0.7         RSQLite_2.0    
 [5] rlang_0.1.1     blob_1.1.0      bit64_0.9-7     bit_1.1-12     
 [9] compiler_3.4.1  pkgconfig_2.0.1 memoise_1.1.0   tibble_1.3.3

 

 

package updates • 799 views
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can you provide an example of a package that you try to install, and that produces this error?

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