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

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:

• https://stat.ethz.ch/pipermail/bioc-devel/2016-April/009142.html
• https://cran.r-project.org/doc/manuals/r-release/NEWS.html (CHANGES IN R 3.3.2, Section Bug Fixes, Item 4)

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