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sigven / oncoEnrichR

Explore the cancer relevance of your gene list
https://sigven.github.io/oncoEnrichR/
MIT License
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Error in loadNamespace(name) : there is no package called ‘assertable’ #3

Closed dpolychr closed 3 years ago

dpolychr commented 3 years ago

Hi @sigven,

Many thanks for this great package! I have successfully installed it and loaded the library without any issues. However going through the example provided I get an error. More specifically, when running:

myc_report <- oncoEnrichR::onco_enrich(query = myc_interact_targets$symbol, show_cell_tissue = T, project_title = "cMYC_BioID_screen", project_owner = "Raught et al.")

I am getting the error:

Error in loadNamespace(name) : there is no package called ‘assertable’

Any help with that would be much appreciated.

Here is my R session:


─ Session info ──────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       macOS Catalina 10.15.7      
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/Athens               
 date     2021-05-14                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────
 package              * version  date       lib source                             
 annotate             * 1.68.0   2020-10-27 [1] Bioconductor                       
 AnnotationDbi        * 1.52.0   2020-10-27 [1] Bioconductor                       
 assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.0.2)                     
 Biobase              * 2.50.0   2020-10-27 [1] Bioconductor                       
 BiocGenerics         * 0.36.1   2021-04-16 [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                 1.0-7    2021-04-24 [1] CRAN (R 4.0.2)                     
 blob                   1.2.1    2020-01-20 [1] CRAN (R 4.0.2)                     
 cachem                 1.0.4    2021-02-13 [1] CRAN (R 4.0.2)                     
 cellranger             1.1.0    2016-07-27 [1] CRAN (R 4.0.2)                     
 cli                    2.5.0    2021-04-26 [1] CRAN (R 4.0.2)                     
 colorspace             2.0-1    2021-05-04 [1] CRAN (R 4.0.2)                     
 crayon                 1.4.1    2021-02-08 [1] CRAN (R 4.0.2)                     
 curl                   4.3.1    2021-04-30 [1] CRAN (R 4.0.2)                     
 data.table             1.14.0   2021-02-21 [1] CRAN (R 4.0.2)                     
 DBI                    1.1.1    2021-01-15 [1] CRAN (R 4.0.2)                     
 DelayedArray           0.16.3   2021-03-24 [1] Bioconductor                       
 dplyr                  1.0.6    2021-05-05 [1] CRAN (R 4.0.2)                     
 ellipsis               0.3.2    2021-04-29 [1] CRAN (R 4.0.2)                     
 ensurer                1.1      2015-04-21 [1] CRAN (R 4.0.2)                     
 fansi                  0.4.2    2021-01-15 [1] CRAN (R 4.0.2)                     
 fastmap                1.1.0    2021-01-25 [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 4.0.5)                     
 generics               0.1.0    2020-10-31 [1] CRAN (R 4.0.2)                     
 GenomeInfoDb         * 1.26.7   2021-04-08 [1] Bioconductor                       
 GenomeInfoDbData       1.2.4    2021-04-21 [1] Bioconductor                       
 GenomicRanges        * 1.42.0   2020-10-27 [1] Bioconductor                       
 ggplot2                3.3.3    2020-12-30 [1] CRAN (R 4.0.2)                     
 glue                   1.4.2    2020-08-27 [1] CRAN (R 4.0.2)                     
 graph                * 1.68.0   2020-10-27 [1] Bioconductor                       
 GSEABase             * 1.52.1   2020-12-11 [1] Bioconductor                       
 gtable                 0.3.0    2019-03-25 [1] CRAN (R 4.0.2)                     
 haven                  2.4.1    2021-04-23 [1] CRAN (R 4.0.2)                     
 hms                    1.0.0    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                       
 janitor                2.1.0    2021-01-05 [1] CRAN (R 4.0.2)                     
 lattice                0.20-41  2020-04-02 [1] CRAN (R 4.0.5)                     
 lifecycle              1.0.0    2021-02-15 [1] CRAN (R 4.0.2)                     
 lubridate              1.7.10   2021-02-26 [1] CRAN (R 4.0.2)                     
 magrittr               2.0.1    2020-11-17 [1] CRAN (R 4.0.2)                     
 Matrix                 1.3-2    2021-01-06 [1] CRAN (R 4.0.5)                     
 MatrixGenerics       * 1.2.1    2021-01-30 [1] Bioconductor                       
 matrixStats          * 0.58.0   2021-01-29 [1] CRAN (R 4.0.2)                     
 memoise                2.0.0    2021-01-26 [1] CRAN (R 4.0.2)                     
 munsell                0.5.0    2018-06-12 [1] CRAN (R 4.0.2)                     
 oncoEnrichR          * 0.9.6    2021-05-14 [1] Github (sigven/oncoEnrichR@48c0b3e)
 openxlsx               4.2.3    2020-10-27 [1] CRAN (R 4.0.2)                     
 org.Hs.eg.db           3.12.0   2021-05-14 [1] Bioconductor                       
 pillar                 1.6.0    2021-04-13 [1] CRAN (R 4.0.2)                     
 pkgconfig              2.0.3    2019-09-22 [1] CRAN (R 4.0.2)                     
 purrr                  0.3.4    2020-04-17 [1] CRAN (R 4.0.2)                     
 R6                     2.5.0    2020-10-28 [1] CRAN (R 4.0.2)                     
 Rcpp                   1.0.6    2021-01-15 [1] CRAN (R 4.0.2)                     
 RCurl                  1.98-1.3 2021-03-16 [1] CRAN (R 4.0.2)                     
 readxl                 1.3.1    2019-03-13 [1] CRAN (R 4.0.2)                     
 rio                    0.5.26   2021-03-01 [1] CRAN (R 4.0.2)                     
 rlang                  0.4.11   2021-04-30 [1] CRAN (R 4.0.2)                     
 RSQLite                2.2.7    2021-04-22 [1] CRAN (R 4.0.2)                     
 S4Vectors            * 0.28.1   2020-12-09 [1] Bioconductor                       
 scales                 1.1.1    2020-05-11 [1] CRAN (R 4.0.2)                     
 sessioninfo            1.1.1    2018-11-05 [1] CRAN (R 4.0.2)                     
 snakecase              0.11.0   2019-05-25 [1] CRAN (R 4.0.2)                     
 solvebio               2.10.1   2021-03-10 [1] CRAN (R 4.0.2)                     
 stringi                1.6.1    2021-05-10 [1] CRAN (R 4.0.2)                     
 stringr                1.4.0    2019-02-10 [1] CRAN (R 4.0.2)                     
 SummarizedExperiment * 1.20.0   2020-10-27 [1] Bioconductor                       
 tibble                 3.1.1    2021-04-18 [1] CRAN (R 4.0.5)                     
 tidyr                  1.1.3    2021-03-03 [1] CRAN (R 4.0.2)                     
 tidyselect             1.1.1    2021-04-30 [1] CRAN (R 4.0.2)                     
 TissueEnrich           1.10.1   2021-04-04 [1] Bioconductor                       
 utf8                   1.2.1    2021-03-12 [1] CRAN (R 4.0.2)                     
 vctrs                  0.3.8    2021-04-29 [1] CRAN (R 4.0.2)                     
 withr                  2.4.2    2021-04-18 [1] CRAN (R 4.0.5)                     
 XML                  * 3.99-0.6 2021-03-16 [1] CRAN (R 4.0.2)                     
 xtable                 1.8-4    2019-04-21 [1] CRAN (R 4.0.2)                     
 XVector                0.30.0   2020-10-28 [1] Bioconductor                       
 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```
dpolychr commented 3 years ago

Update on this: Installing assertable from CRAN seems to have solved the issue and the code is running now :-)

sigven commented 3 years ago

hi @dpolychr,

Thanks for the notification. Will check why assertable was not installed as a dependency in the first place.

kind regards, Sigve