pqsfinder gives: invalid class “PQSViews” object: undefined class for slot "elementMetadata" error message
1
0
Entering edit mode
hwu12 ▴ 10
@hwu12-12353
Last seen 23 months ago
United States

I installed the pqsfinder package but cannot run the example code. Any suggestions? Thanks!!!

pqsfinder(DNAString("CCCCCCGGGTGGGTGGGTGGGTAAAA"))

Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Error in pqsfinder(DNAString("CCCCCCGGGTGGGTGGGTGGGTAAAA")) : 
Evaluation error: invalid class “PQSViews” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL").
sessionInfo( )

─ Session info ──────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       macOS Catalina 10.15.7      
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Toronto             
 date     2021-02-09                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────
 ! package              * version  date       lib source                              
   abind                  1.4-5    2016-07-21 [1] CRAN (R 4.0.2)                      
   AnnotationDbi        * 1.52.0   2020-10-27 [1] Bioconductor                        
   askpass                1.1      2019-01-13 [1] CRAN (R 4.0.0)                      
   assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.0.0)                      
   backports              1.2.1    2020-12-09 [1] CRAN (R 4.0.2)                      
   Biobase              * 2.50.0   2020-10-27 [1] Bioconductor                        
   BiocFileCache          1.14.0   2020-10-27 [1] Bioconductor                        
   BiocGenerics         * 0.36.0   2020-10-27 [1] Bioconductor                        
   BiocManager            1.30.10  2019-11-16 [1] CRAN (R 4.0.2)                      
   BiocParallel           1.24.1   2020-11-06 [1] Bioconductor                        
   biomaRt                2.46.0   2020-10-27 [1] Bioconductor                        
   Biostrings           * 2.58.0   2020-10-27 [1] Bioconductor                        
   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)                      
   bitops                 1.0-6    2013-08-17 [1] CRAN (R 4.0.0)                      
   blob                   1.2.1    2020-01-20 [1] CRAN (R 4.0.0)                      
   broom                  0.7.4    2021-01-29 [1] CRAN (R 4.0.2)                      
   callr                  3.5.1    2020-10-13 [1] CRAN (R 4.0.2)                      
   car                    3.0-10   2020-09-29 [1] CRAN (R 4.0.2)                      
   carData                3.0-4    2020-05-22 [1] CRAN (R 4.0.2)                      
   cellranger             1.1.0    2016-07-27 [1] CRAN (R 4.0.0)                      
 V cli                    2.2.0    2021-01-31 [1] CRAN (R 4.0.2)                      
   colorspace             2.0-0    2020-11-11 [1] CRAN (R 4.0.2)                      
 V crayon                 1.3.4    2021-02-08 [1] CRAN (R 4.0.3)                      
   curl                   4.3      2019-12-02 [1] CRAN (R 4.0.0)                      
   data.table             1.13.6   2020-12-30 [1] CRAN (R 4.0.2)                      
 V DBI                    1.1.0    2021-01-15 [1] CRAN (R 4.0.2)                      
 V dbplyr                 2.0.0    2021-02-03 [1] CRAN (R 4.0.2)                      
   DelayedArray           0.16.0   2020-10-27 [1] Bioconductor                        
   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                 0.6.27   2020-10-24 [1] CRAN (R 4.0.2)                      
 V dplyr                  1.0.2    2021-02-02 [1] CRAN (R 4.0.2)                      
   ellipsis               0.3.1    2020-05-15 [1] CRAN (R 4.0.0)                      
 V fansi                  0.4.1    2021-01-15 [1] CRAN (R 4.0.2)                      
   forcats                0.5.1    2021-01-27 [1] CRAN (R 4.0.2)                      
   foreign                0.8-81   2020-12-22 [1] CRAN (R 4.0.2)                      
   fs                     1.5.0    2020-07-31 [1] CRAN (R 4.0.2)                      
   generics               0.1.0    2020-10-31 [1] CRAN (R 4.0.2)                      
   GenomeInfoDb         * 1.26.2   2020-12-08 [1] Bioconductor                        
   GenomeInfoDbData       1.2.4    2020-12-18 [1] Bioconductor                        
   GenomicAlignments      1.26.0   2020-10-27 [1] Bioconductor                        
   GenomicFeatures      * 1.42.1   2020-11-11 [1] Bioconductor                        
   GenomicRanges        * 1.42.0   2020-10-27 [1] Bioconductor                        
   ggplot2              * 3.3.3    2020-12-30 [1] CRAN (R 4.0.2)                      
   ggpubr               * 0.4.0    2020-06-27 [1] CRAN (R 4.0.2)                      
   ggseqlogo            * 0.1      2020-08-06 [1] Github (omarwagih/ggseqlogo@4adc8f2)
   ggsignif               0.6.0    2019-08-08 [1] CRAN (R 4.0.2)                      
   glue                   1.4.2    2020-08-27 [1] CRAN (R 4.0.2)                      
   gtable                 0.3.0    2019-03-25 [1] CRAN (R 4.0.0)                      
   haven                  2.3.1    2020-06-01 [1] CRAN (R 4.0.0)                      
 V hms                    0.5.3    2021-01-13 [1] CRAN (R 4.0.2)                      
   httr                   1.4.2    2020-07-20 [1] CRAN (R 4.0.2)                      
   IRanges              * 2.24.1   2020-12-12 [1] Bioconductor                        
   lattice                0.20-41  2020-04-02 [1] CRAN (R 4.0.3)                      
   lifecycle              0.2.0    2020-03-06 [1] CRAN (R 4.0.0)                      
   magrittr               2.0.1    2020-11-17 [1] CRAN (R 4.0.2)                      
 V Matrix                 1.3-0    2021-01-06 [1] CRAN (R 4.0.2)                      
   MatrixGenerics         1.2.0    2020-10-27 [1] Bioconductor                        
 V matrixStats            0.57.0   2021-01-29 [1] CRAN (R 4.0.2)                      
 V memoise                1.1.0    2021-01-26 [1] CRAN (R 4.0.2)                      
   munsell                0.5.0    2018-06-12 [1] CRAN (R 4.0.0)                      
   openssl                1.4.3    2020-09-18 [1] CRAN (R 4.0.2)                      
   openxlsx               4.2.3    2020-10-27 [1] CRAN (R 4.0.2)                      
   pillar                 1.4.7    2020-11-20 [1] CRAN (R 4.0.2)                      
   pkgbuild               1.2.0    2020-12-15 [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)                      
   pqsfinder            * 2.4.0    2020-04-27 [1] Bioconductor                        
   prettyunits            1.1.1    2020-01-24 [1] CRAN (R 4.0.0)                      
   processx               3.4.5    2020-11-30 [1] CRAN (R 4.0.2)                      
   progress               1.2.2    2019-05-16 [1] CRAN (R 4.0.0)                      
   ps                     1.5.0    2020-12-05 [1] CRAN (R 4.0.2)                      
   purrr                  0.3.4    2020-04-17 [1] CRAN (R 4.0.0)                      
   R6                     2.5.0    2020-10-28 [1] CRAN (R 4.0.2)                      
 V rappdirs               0.3.1    2021-01-31 [1] CRAN (R 4.0.2)                      
 V Rcpp                   1.0.5    2021-01-15 [1] CRAN (R 4.0.2)                      
   RCurl                  1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)                      
   readxl                 1.3.1    2019-03-13 [1] CRAN (R 4.0.0)                      
   remotes                2.2.0    2020-07-21 [1] CRAN (R 4.0.2)                      
   rio                    0.5.16   2018-11-26 [1] CRAN (R 4.0.2)                      
   rlang                  0.4.10   2020-12-30 [1] CRAN (R 4.0.2)                      
   rprojroot              2.0.2    2020-11-15 [1] CRAN (R 4.0.2)                      
   Rsamtools            * 2.6.0    2020-10-27 [1] Bioconductor                        
 V RSQLite                2.2.2    2021-01-24 [1] CRAN (R 4.0.2)                      
   rstatix                0.6.0    2020-06-18 [1] CRAN (R 4.0.2)                      
   rstudioapi             0.13     2020-11-12 [1] CRAN (R 4.0.2)                      
   rtracklayer          * 1.50.0   2020-10-27 [1] Bioconductor                        
   S4Vectors            * 0.28.1   2020-12-09 [1] Bioconductor                        
   scales                 1.1.1    2020-05-11 [1] CRAN (R 4.0.0)                      
   sessioninfo            1.1.1    2018-11-05 [1] CRAN (R 4.0.0)                      
   stringi                1.5.3    2020-09-09 [1] CRAN (R 4.0.2)                      
   stringr                1.4.0    2019-02-10 [1] CRAN (R 4.0.0)                      
   SummarizedExperiment   1.20.0   2020-10-27 [1] Bioconductor                        
   testthat               3.0.1    2020-12-17 [1] CRAN (R 4.0.3)                      
 V tibble                 3.0.4    2021-01-29 [1] CRAN (R 4.0.2)                      
   tidyr                  1.1.2    2020-08-27 [1] CRAN (R 4.0.2)                      
   tidyselect             1.1.0    2020-05-11 [1] CRAN (R 4.0.0)                      
   usethis              * 2.0.0    2020-12-10 [1] CRAN (R 4.0.2)                      
   vctrs                  0.3.6    2020-12-17 [1] CRAN (R 4.0.3)                      
   withr                  2.4.1    2021-01-26 [1] CRAN (R 4.0.2)                      
   XML                    3.99-0.5 2020-07-23 [1] CRAN (R 4.0.2)                      
   xml2                   1.3.2    2020-04-23 [1] CRAN (R 4.0.0)                      
   XVector              * 0.30.0   2020-10-28 [1] Bioconductor                        
   yaml                   2.2.1    2020-02-01 [1] CRAN (R 4.0.0)                      
   zip                    2.1.1    2020-08-27 [1] CRAN (R 4.0.2)                      
   zlibbioc               1.36.0   2020-10-28 [1] Bioconductor                        

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

 V ── Loaded and on-disk version mismatch.
pqsfinder • 917 views
ADD COMMENT
1
Entering edit mode
jiri.hon ▴ 10
@jirihon-7904
Last seen 3.8 years ago
Czech Republic

Please update to the latest Bioconductor (see https://bioconductor.org/install/). You probably have some packages in incompatible versions. The current pqsfinder is 2.6.0 (Bioconductor 3.12) and it should run fine.

ADD COMMENT
0
Entering edit mode

You are right! Thanks a lot!!!

ADD REPLY

Login before adding your answer.

Traffic: 803 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6