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Error that impacts BioCor #32

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llrs opened this issue Oct 22, 2020 · 5 comments
Closed

Error that impacts BioCor #32

llrs opened this issue Oct 22, 2020 · 5 comments

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@llrs
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llrs commented Oct 22, 2020 •
edited
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Hi,
I am the developer of BioCor that suggest and uses GOSemSim on the vignette.

On the latest Bioconductor (the soon to be released 3.12) I got an error on the vignette that I think is raises from GOSemSim. Find below a reproducible example on R 4.0.3:

gene_ids <- c("23098", "4843", "5431", "4710", "4287", "5217", "7321", "1207", 
  "9891", "27252", "56922", "1136", "51668", "5241", "54700", "43", 
  "11020", "5372", "7528", "79913", "2717", "6650", "9738", "3718", 
  "9827", "23586", "9148", "975", "84274", "80824", "8078", "10686", 
  "6152", "374291", "60482", "6509", "2582", "10560", "9194", "5228", 
  "25950", "10564", "26212", "8189", "94101", "8520", "968", "4301", 
  "2643", "51763", "23164", "254428", "29079", "56886", "9380", 
  "85465", "2247", "254013", "54509", "4123", "3801", "27043", 
  "10907", "84958", "26230", "9589", "908", "27147", "6129", "6749", 
  "2308", "7069", "3628", "5352", "1525", "58494", "9337", "7273", 
  "10670", "138199", "6750", "26958", "136227", "29115", "51005", 
  "7086", "285231", "4724", "9232", "1020", "2923", "124975", "55048", 
  "55867", "3516", "9677", "3965", "6940", "27258", "3866", "54811", 
  "5707", "201626", "7025", "10458", "127064", "126375", "9735", 
  "3852", "388567", "55615", "401541", "388552", "728", "5660", 
  "5336", "8337", "5004", "3833", "26063", "51750", "3690", "92335"
)
library("GOSemSim")
library("org.Hs.eg.db")
BP <- godata("org.Hs.eg.db", ont = "BP", computeIC = TRUE)
gsGO <- GOSemSim::mgeneSim(gene_ids, semData = BP, measure = "Resnik", verbose = TRUE)

The error as you can see below seems to be related to changes on Rcpp:

Error in infoContentMethod_cpp(ID1, ID2, .anc, IC, method, ont) :
Expecting a string vector: [type=logical; required=STRSXP].
traceback()
6: stop(structure(list(message = "Expecting a string vector: [type=logical; required=STRSXP].",
call = infoContentMethod_cpp(ID1, ID2, .anc, IC, method,
ont), cppstack = NULL), class = c("Rcpp::not_compatible",
"C++Error", "error", "condition")))
5: infoContentMethod_cpp(ID1, ID2, .anc, IC, method, ont)
4: infoContentMethod(t1, t2, method = method, semData)
3: termSim(GO1, GO2, semData, method = measure)
2: mgoSim(uniqueGO, uniqueGO, semData, measure = measure, combine = NULL)
1: GOSemSim::mgeneSim(a, semData = BP, measure = "Resnik", verbose = TRUE)

Session Info 
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Ubuntu 20.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Madrid               
 date     2020-10-22                  

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package              * version  date       lib source        
   airway               * 1.9.0    2020-04-30 [1] Bioconductor  
   annotate               1.67.2   2020-10-15 [1] Bioconductor  
   AnnotationDbi        * 1.51.3   2020-07-25 [1] Bioconductor  
   assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.0.3)
   backports              1.1.10   2020-09-15 [1] CRAN (R 4.0.3)
   base64enc              0.1-3    2015-07-28 [1] CRAN (R 4.0.3)
   Biobase              * 2.49.1   2020-09-03 [1] Bioconductor  
   BiocGenerics         * 0.35.4   2020-06-04 [1] Bioconductor  
   BiocManager            1.30.10  2019-11-16 [1] CRAN (R 4.0.3)
 P BioCor               * 1.13.1   2020-10-13 [?] Bioconductor  
   BiocParallel           1.23.3   2020-10-17 [1] Bioconductor  
   bit                    4.0.4    2020-08-04 [1] CRAN (R 4.0.3)
   bit64                  4.0.5    2020-08-30 [1] CRAN (R 4.0.3)
   bitops                 1.0-6    2013-08-17 [1] CRAN (R 4.0.3)
   blob                   1.2.1    2020-01-20 [1] CRAN (R 4.0.3)
   boot                 * 1.3-25   2020-04-26 [1] CRAN (R 4.0.3)
   callr                  3.5.1    2020-10-13 [1] CRAN (R 4.0.3)
   checkmate              2.0.0    2020-02-06 [1] CRAN (R 4.0.3)
   cli                    2.1.0    2020-10-12 [1] CRAN (R 4.0.3)
   cluster                2.1.0    2019-06-19 [1] CRAN (R 4.0.3)
   codetools              0.2-16   2018-12-24 [1] CRAN (R 4.0.3)
   colorspace             1.4-1    2019-03-18 [1] CRAN (R 4.0.3)
   crayon                 1.3.4    2017-09-16 [1] CRAN (R 4.0.3)
   data.table             1.13.2   2020-10-19 [1] CRAN (R 4.0.3)
   DBI                    1.1.0    2019-12-15 [1] CRAN (R 4.0.3)
   DelayedArray           0.15.16  2020-10-06 [1] Bioconductor  
   desc                   1.2.0    2018-05-01 [1] CRAN (R 4.0.3)
   DESeq2               * 1.29.16  2020-10-13 [1] Bioconductor  
   devtools             * 2.3.2    2020-09-18 [1] CRAN (R 4.0.3)
   digest                 0.6.26   2020-10-17 [1] CRAN (R 4.0.3)
   ellipsis               0.3.1    2020-05-15 [1] CRAN (R 4.0.3)
   evaluate               0.14     2019-05-28 [1] CRAN (R 4.0.3)
   fansi                  0.4.1    2020-01-08 [1] CRAN (R 4.0.3)
   foreign                0.8-80   2020-05-24 [1] CRAN (R 4.0.3)
   Formula              * 1.2-4    2020-10-16 [1] CRAN (R 4.0.3)
   fs                     1.5.0    2020-07-31 [1] CRAN (R 4.0.3)
   genefilter             1.71.0   2020-04-27 [1] Bioconductor  
   geneplotter            1.67.0   2020-04-27 [1] Bioconductor  
   GenomeInfoDb         * 1.25.11  2020-09-03 [1] Bioconductor  
   GenomeInfoDbData       1.2.4    2020-10-22 [1] Bioconductor  
   GenomicRanges        * 1.41.6   2020-08-12 [1] Bioconductor  
   ggplot2              * 3.3.2    2020-06-19 [1] CRAN (R 4.0.3)
   glue                   1.4.2    2020-08-27 [1] CRAN (R 4.0.3)
   GO.db                  3.12.0   2020-10-22 [1] Bioconductor  
   GOSemSim             * 2.15.2   2020-09-04 [1] Bioconductor  
   graph                  1.67.1   2020-05-27 [1] Bioconductor  
   gridExtra              2.3      2017-09-09 [1] CRAN (R 4.0.3)
   GSEABase               1.51.1   2020-05-29 [1] Bioconductor  
   gtable                 0.3.0    2019-03-25 [1] CRAN (R 4.0.3)
   highr                  0.8      2019-03-20 [1] CRAN (R 4.0.3)
   Hmisc                * 4.4-1    2020-08-10 [1] CRAN (R 4.0.3)
   htmlTable              2.1.0    2020-09-16 [1] CRAN (R 4.0.3)
   htmltools              0.5.0    2020-06-16 [1] CRAN (R 4.0.3)
   htmlwidgets            1.5.2    2020-10-03 [1] CRAN (R 4.0.3)
   httr                   1.4.2    2020-07-20 [1] CRAN (R 4.0.3)
   IRanges              * 2.23.10  2020-06-13 [1] Bioconductor  
   jpeg                   0.1-8.1  2019-10-24 [1] CRAN (R 4.0.3)
   knitr                  1.30     2020-09-22 [1] CRAN (R 4.0.3)
   lattice              * 0.20-41  2020-04-02 [1] CRAN (R 4.0.3)
   latticeExtra           0.6-29   2019-12-19 [1] CRAN (R 4.0.3)
   lifecycle              0.2.0    2020-03-06 [1] CRAN (R 4.0.3)
   locfit                 1.5-9.4  2020-03-25 [1] CRAN (R 4.0.3)
   magrittr               1.5      2014-11-22 [1] CRAN (R 4.0.3)
   Matrix                 1.2-18   2019-11-27 [1] CRAN (R 4.0.3)
   MatrixGenerics       * 1.1.8    2020-10-20 [1] Bioconductor  
   matrixStats          * 0.57.0   2020-09-25 [1] CRAN (R 4.0.3)
   memoise                1.1.0    2017-04-21 [1] CRAN (R 4.0.3)
   munsell                0.5.0    2018-06-12 [1] CRAN (R 4.0.3)
   nnet                   7.3-14   2020-04-26 [1] CRAN (R 4.0.3)
   org.Hs.eg.db         * 3.12.0   2020-10-22 [1] Bioconductor  
   pillar                 1.4.6    2020-07-10 [1] CRAN (R 4.0.3)
   pkgbuild               1.1.0    2020-07-13 [1] CRAN (R 4.0.3)
   pkgconfig              2.0.3    2019-09-22 [1] CRAN (R 4.0.3)
   pkgload                1.1.0    2020-05-29 [1] CRAN (R 4.0.3)
   png                    0.1-7    2013-12-03 [1] CRAN (R 4.0.3)
   prettyunits            1.1.1    2020-01-24 [1] CRAN (R 4.0.3)
   processx               3.4.4    2020-09-03 [1] CRAN (R 4.0.3)
   ps                     1.4.0    2020-10-07 [1] CRAN (R 4.0.3)
   R6                     2.4.1    2019-11-12 [1] CRAN (R 4.0.3)
   RColorBrewer           1.1-2    2014-12-07 [1] CRAN (R 4.0.3)
   Rcpp                   1.0.5    2020-07-06 [1] CRAN (R 4.0.3)
   RCurl                  1.98-1.2 2020-04-18 [1] CRAN (R 4.0.3)
   reactome.db            1.74.0   2020-10-22 [1] Bioconductor  
   remotes                2.2.0    2020-07-21 [1] CRAN (R 4.0.3)
   rlang                  0.4.8    2020-10-08 [1] CRAN (R 4.0.3)
   rmarkdown              2.5      2020-10-21 [1] CRAN (R 4.0.3)
   rpart                  4.1-15   2019-04-12 [1] CRAN (R 4.0.3)
   rprojroot              1.3-2    2018-01-03 [1] CRAN (R 4.0.3)
   RSQLite                2.2.1    2020-09-30 [1] CRAN (R 4.0.3)
   rstudioapi             0.11     2020-02-07 [1] CRAN (R 4.0.3)
   S4Vectors            * 0.27.14  2020-10-09 [1] Bioconductor  
   scales                 1.1.1    2020-05-11 [1] CRAN (R 4.0.3)
   sessioninfo            1.1.1    2018-11-05 [1] CRAN (R 4.0.3)
   stringi                1.5.3    2020-09-09 [1] CRAN (R 4.0.3)
   stringr                1.4.0    2019-02-10 [1] CRAN (R 4.0.3)
   SummarizedExperiment * 1.19.9   2020-10-01 [1] Bioconductor  
   survival             * 3.2-7    2020-09-28 [1] CRAN (R 4.0.3)
   targetscan.Hs.eg.db  * 0.6.1    2020-10-22 [1] Bioconductor  
   testthat             * 2.3.2    2020-03-02 [1] CRAN (R 4.0.3)
   tibble                 3.0.4    2020-10-12 [1] CRAN (R 4.0.3)
   usethis              * 1.6.3    2020-09-17 [1] CRAN (R 4.0.3)
   vctrs                  0.3.4    2020-08-29 [1] CRAN (R 4.0.3)
   withr                  2.3.0    2020-09-22 [1] CRAN (R 4.0.3)
   xfun                   0.18     2020-09-29 [1] CRAN (R 4.0.3)
   XML                    3.99-0.5 2020-07-23 [1] CRAN (R 4.0.3)
   xtable                 1.8-4    2019-04-21 [1] CRAN (R 4.0.3)
   XVector                0.29.3   2020-06-25 [1] Bioconductor  
   yaml                   2.2.1    2020-02-01 [1] CRAN (R 4.0.3)
   zlibbioc               1.35.0   2020-04-27 [1] Bioconductor

Many thanks!
@GuangchuangYu
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cannot reproduce your issue:

> BP <- godata("org.Hs.eg.db", ont = "BP", computeIC = TRUE)
preparing gene to GO mapping data...
preparing IC data...

> gsGO <- GOSemSim::mgeneSim(gene_ids, semData = BP, measure = "Resnik", verbose = TRUE)
  |======================================================================| 100%
> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Arch Linux                  
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Asia/Chongqing              
 date     2020-10-23                  

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version date       lib source        
 AnnotationDbi * 1.50.3  2020-07-25 [1] Bioconductor  
 assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
 backports       1.1.10  2020-09-15 [1] CRAN (R 4.0.2)
 Biobase       * 2.48.0  2020-04-27 [1] Bioconductor  
 BiocGenerics  * 0.34.0  2020-04-27 [1] Bioconductor  
 BiocManager     1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
 bit             4.0.4   2020-08-04 [1] CRAN (R 4.0.2)
 bit64           4.0.5   2020-08-30 [1] CRAN (R 4.0.2)
 blob            1.2.1   2020-01-20 [1] CRAN (R 4.0.0)
 callr           3.5.1   2020-10-13 [1] CRAN (R 4.0.3)
 cli             2.1.0   2020-10-12 [1] CRAN (R 4.0.3)
 conflicted    * 1.0.4   2019-06-21 [1] CRAN (R 4.0.0)
 crayon          1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
 DBI             1.1.0   2019-12-15 [1] CRAN (R 4.0.0)
 desc            1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
 devtools        2.3.2   2020-09-18 [1] CRAN (R 4.0.2)
 digest          0.6.26  2020-10-17 [1] CRAN (R 4.0.3)
 ellipsis        0.3.1   2020-05-15 [1] CRAN (R 4.0.0)
 fansi           0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
 fs              1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
 glue            1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
 GO.db           3.11.4  2020-06-15 [1] Bioconductor  
 GOSemSim      * 2.15.2  2020-10-23 [1] Bioconductor  
 IRanges       * 2.22.2  2020-05-21 [1] Bioconductor  
 magrittr      * 1.5     2014-11-22 [1] CRAN (R 4.0.0)
 memoise         1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
 org.Hs.eg.db  * 3.11.4  2020-06-15 [1] Bioconductor  
 pkgbuild        1.1.0   2020-07-13 [1] CRAN (R 4.0.2)
 pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.0.0)
 pkgload         1.1.0   2020-05-29 [1] CRAN (R 4.0.0)
 prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
 processx        3.4.4   2020-09-03 [1] CRAN (R 4.0.2)
 ps              1.4.0   2020-10-07 [1] CRAN (R 4.0.2)
 R6              2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 Rcpp            1.0.5   2020-07-06 [1] CRAN (R 4.0.2)
 remotes         2.2.0   2020-07-21 [1] CRAN (R 4.0.2)
 rlang           0.4.8   2020-10-08 [1] CRAN (R 4.0.2)
 rprojroot       1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
 RSQLite         2.2.1   2020-09-30 [1] CRAN (R 4.0.2)
 rvcheck       * 0.1.8   2020-04-26 [1] local         
 S4Vectors     * 0.26.1  2020-05-16 [1] Bioconductor  
 sessioninfo     1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
 testthat        2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
 usethis         1.6.3   2020-09-17 [1] CRAN (R 4.0.2)
 vctrs           0.3.4   2020-08-29 [1] CRAN (R 4.0.2)
 wget          * 0.0.1   2020-04-27 [1] local         
 withr           2.3.0   2020-09-22 [1] CRAN (R 4.0.2)

@llrs
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llrs commented Oct 23, 2020

There are several differences on the session info. The most notable ones are the org.Hs.eg.db version you are using 3.11.4 while I am using 3.12.0, Biobase version is also higher (2.49.1 to 2.48) on my omputer as well as BiocGenerics (0.35.4 to 0.34.0).

Did you install them using BiocManager::install(version = "3.12") ?

@GuangchuangYu
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GuangchuangYu commented Oct 29, 2020 •
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should be fixed in GOSemSim v >= 2.16.1

@llrs
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llrs commented Oct 29, 2020

Great! Have this been imported to the master and RELEASE_3_12 branch? I ask because I want to reactivated a code chunk from a vignette on BioCor.
Would it be possible to add some tests to catch this kind of errors on the future earlier?

@GuangchuangYu
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already push to 3.12 branch.

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@GuangchuangYu @llrs