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Question: Found more than one class
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gravatar for Kamil Slowikowski
26 days ago by
United States
Kamil Slowikowski20 wrote:

Problem

I get 6 identical warning messages when I open a new file connection.

Expected behavior

asdf <- base::file("asdf.txt")

There should be no warnings. I asked for the file function from the base package by using the :: syntax, so there should be no ambiguity about which function to run.

Actual behavior

Run the same code after loading two packages:

library(oligo)
library(RJSONIO)
asdf <- base::file("asdf.txt")

Instead of no warnings, I get the same warning 6 times:

Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’

Similar issues

You can find many duplicates of this issue all over the web: forums, github issues, published documentation, etc.

Just search for: "found more than one class" r

Unfortunately, I can't find any suggested solutions for this problem.

sessionInfo

> devtools::session_info()
Session info --------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.0 (2017-04-21)
 system   x86_64, darwin15.6.0        
 ui       RStudio (1.0.153)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2017-11-23                  

Packages ------------------------------------------------------------------------------------------------------------------------
 package              * version  date       source         
 affxparser             1.48.0   2017-04-25 Bioconductor   
 affyio                 1.46.0   2017-04-25 Bioconductor   
 base                 * 3.4.0    2017-04-21 local          
 Biobase              * 2.36.2   2017-05-04 cran (@2.36.2) 
 BiocGenerics         * 0.22.0   2017-04-25 cran (@0.22.0) 
 BiocInstaller          1.26.1   2017-09-01 Bioconductor   
 Biostrings           * 2.44.0   2017-04-25 Bioconductor   
 bit                    1.1-12   2014-04-09 CRAN (R 3.4.0) 
 bitops                 1.0-6    2013-08-17 CRAN (R 3.4.0) 
 codetools              0.2-15   2016-10-05 CRAN (R 3.4.0) 
 compiler               3.4.0    2017-04-21 local          
 datasets             * 3.4.0    2017-04-21 local          
 DBI                    0.6-1    2017-04-01 CRAN (R 3.4.0) 
 DelayedArray           0.2.0    2017-04-25 Bioconductor   
 devtools               1.13.0   2017-05-08 CRAN (R 3.4.0) 
 digest                 0.6.12   2017-01-27 CRAN (R 3.4.0) 
 ff                     2.2-13   2014-04-09 CRAN (R 3.4.0) 
 foreach                1.4.3    2015-10-13 CRAN (R 3.4.0) 
 GenomeInfoDb           1.12.0   2017-04-25 Bioconductor   
 GenomeInfoDbData       0.99.0   2017-05-02 Bioconductor   
 GenomicRanges          1.28.0   2017-04-25 Bioconductor   
 graphics             * 3.4.0    2017-04-21 local          
 grDevices            * 3.4.0    2017-04-21 local          
 grid                   3.4.0    2017-04-21 local          
 IRanges              * 2.9.19   2017-04-17 Bioconductor   
 iterators              1.0.8    2015-10-13 CRAN (R 3.4.0) 
 lattice                0.20-35  2017-03-25 CRAN (R 3.4.0) 
 Matrix                 1.2-10   2017-04-28 CRAN (R 3.4.0) 
 matrixStats            0.52.2   2017-04-14 CRAN (R 3.4.0) 
 memoise                1.1.0    2017-04-21 CRAN (R 3.4.0) 
 methods              * 3.4.0    2017-04-21 local          
 oligo                * 1.40.1   2017-05-06 Bioconductor   
 oligoClasses         * 1.38.0   2017-04-25 Bioconductor   
 parallel             * 3.4.0    2017-04-21 local          
 preprocessCore         1.38.0   2017-04-25 Bioconductor   
 Rcpp                   0.12.13  2017-09-28 cran (@0.12.13)
 RCurl                  1.95-4.8 2016-03-01 CRAN (R 3.4.0) 
 RJSONIO              * 1.3-0    2014-07-28 CRAN (R 3.4.0) 
 RSQLite                1.1-2    2017-01-08 CRAN (R 3.4.0) 
 S4Vectors            * 0.13.17  2017-04-23 Bioconductor   
 splines                3.4.0    2017-04-21 local          
 stats                * 3.4.0    2017-04-21 local          
 stats4               * 3.4.0    2017-04-21 local          
 SummarizedExperiment   1.6.0    2017-04-25 Bioconductor   
 tools                  3.4.0    2017-04-21 local          
 utils                * 3.4.0    2017-04-21 local          
 withr                  2.1.0    2017-11-01 CRAN (R 3.4.2) 
 XVector              * 0.16.0   2017-04-25 Bioconductor   
 zlibbioc               1.21.0   2017-04-17 Bioconductor
ADD COMMENTlink modified 19 days ago • written 26 days ago by Kamil Slowikowski20
1

What is your devtools::session_info() ?

ADD REPLYlink written 26 days ago by Wolfgang Huber13k

Yes, your sessionInfo() would help me reproduce this. Right now I can't.

ADD REPLYlink written 22 days ago by Hervé Pagès ♦♦ 13k
1
gravatar for Wolfgang Huber
19 days ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

FWIW this appears to be related to a bug in class handling in an older (outdated) version of R, which Michael or someone recently fixed:

As usual, Kamil and everyone else could save a lot of time by using up-to-date versions and providing session info.

 

ADD COMMENTlink written 19 days ago by Wolfgang Huber13k

I guess you're suggesting that this bug is expected to appear prior to version 3.3.2 and it should not appear in version 3.4.0 (my version). Is that right?

ADD REPLYlink written 19 days ago by Kamil Slowikowski20
1

The example in your original post works fine for me, running on R 3.4.2 with RJSONIO 1.3-0 and oligo 1.42.0. Probably best to try again after updating to the latest versions of R and Bioconductor/CRAN packages.

ADD REPLYlink modified 19 days ago • written 19 days ago by Aaron Lun17k
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