leeprichman
commented
4 years ago Hi Rajendra,
The current CRAN version of magrittr (1.5) is behind the tidyverse/magrittr repository version (1.5.0 or greater) and does not always correctly handle piping to namespaced::functions without parentheticals at the end. It is not compatible with the source code for antigen.garnish. Please follow the instructions in the warning message, and rundevtools::install_github("tidyverse/magrittr") to update to 1.5.0 or greater and then you can test the package with testthat::test_package("antigen.garnish").
Please let me know if the issue persists.
ShahiRB
Hi guys,
Can you do a favor to sort out this issue. I got an error regarding magrittr version though magrittr_1.5 is used:
script used:
> vcf<-"/dir/foo.snpEff.vcf" > garnish_variants(vcf,tumor_sample_name ="foo_tumor_dna")
Error: Loading required package: stringr Error in check_dep_versions() : magrittr version >= 1.5.0 is required and can be installed with: devtools::install_github("tidyverse/magrittr")
> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /theia/home/apps/CO7/skylake/software/OpenBLAS/0.3.5-GCC-8.2.0-2.31.1/lib/libopenblas_skylakexp-r0.3.5.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] antigen.garnish_1.1.0 data.table_1.12.2 magrittr_1.5
loaded via a namespace (and not attached): [1] mclust_5.4.3 Rcpp_1.0.1 ape_5.3 [4] lattice_0.20-38 tidyr_0.8.3 listenv_0.7.0 [7] zoo_1.8-5 Biostrings_2.52.0 assertthat_0.2.1 [10] digest_0.6.19 R6_2.4.0 cellranger_1.1.0 [13] plyr_1.8.4 stats4_3.6.0 ggplot2_3.1.1 [16] pillar_1.4.1 Rdpack_0.11-0 zlibbioc_1.30.0 [19] rlang_0.3.4 lazyeval_0.2.2 curl_3.3 [22] readxl_1.3.1 uuid_0.1-2 vegan_2.5-5 [25] S4Vectors_0.22.0 Matrix_1.2-17 splines_3.6.0 [28] pinfsc50_1.1.0 stringr_1.4.0 foreign_0.8-71 [31] munsell_0.5.0 compiler_3.6.0 xfun_0.7 [34] pkgconfig_2.0.2 BiocGenerics_0.30.0 mgcv_1.8-28 [37] globals_0.12.4 tidyselect_0.2.5 tibble_2.1.3 [40] IRanges_2.18.1 rio_0.5.16 codetools_0.2-16 [43] viridisLite_0.3.0 permute_0.9-5 future_1.13.0 [46] crayon_1.3.4 dplyr_0.8.1 MASS_7.3-51.4 [49] grid_3.6.0 nlme_3.1-140 gtable_0.3.0 [52] scales_1.0.0 bibtex_0.4.2 zip_2.0.2 [55] future.apply_1.3.0 stringi_1.4.3 XVector_0.24.0 [58] vcfR_1.8.0 testthat_2.1.1 openxlsx_4.1.0.1 [61] tools_3.6.0 forcats_0.4.0 glue_1.3.1 [64] purrr_0.3.2 hms_0.4.2 parallel_3.6.0 [67] dt.inflix_0.0.1 colorspace_1.4-1 cluster_2.0.9 [70] gbRd_0.4-11 knitr_1.23 haven_2.1.0
Regards, Rajendra