HiraDatascience
commented
2 months ago I installed it from BiocManager::install("maftools") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.1 (2023-06-16 ucrt) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.3.1/library packages: boot, cluster, codetools, foreign, KernSmooth, lattice, mgcv, nlme, rpart, spatial, survival Old packages: 'BiocManager', 'cachem', 'cli', 'colorspace', 'corrplot', 'cpp11', 'curl', 'data.table', 'digest', 'dplyr', 'fansi', 'farver', 'fastmap', 'fs', 'gert', 'glue', 'gmp', 'htmltools', 'httpuv', 'httr2', 'insight', 'minqa', 'mvtnorm', 'NMF', 'openssl', 'promises', 'Rcpp', 'RcppEigen', 'rlang', 'rmarkdown', 'stringi', 'vctrs', 'waldo', 'xfun' Update all/some/none? [a/s/n]: a Warning: packages ‘data.table’, ‘dplyr’ are in use and will not be installed
There are binary versions available but the source versions are later: binary source needs_compilation cpp11 0.4.7 0.5.0 FALSE curl 5.2.1 5.2.2 TRUE
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/minqa_1.2.8.zip' Content type 'application/zip' length 459712 bytes (448 KB) downloaded 448 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/mvtnorm_1.2-6.zip' Content type 'application/zip' length 785571 bytes (767 KB) downloaded 767 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/NMF_0.28.zip' Content type 'application/zip' length 3104944 bytes (3.0 MB) downloaded 3.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/openssl_2.2.1.zip' Content type 'application/zip' length 3399224 bytes (3.2 MB) downloaded 3.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/promises_1.3.0.zip' Content type 'application/zip' length 2023388 bytes (1.9 MB) downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/Rcpp_1.0.13.zip' Content type 'application/zip' length 2886369 bytes (2.8 MB) downloaded 2.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/RcppEigen_0.3.4.0.2.zip' Content type 'application/zip' length 2612428 bytes (2.5 MB) downloaded 2.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/rlang_1.1.4.zip' Content type 'application/zip' length 1579343 bytes (1.5 MB) downloaded 1.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/rmarkdown_2.28.zip' Content type 'application/zip' length 2683630 bytes (2.6 MB) downloaded 2.6 MB
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/xfun_0.47.zip' Content type 'application/zip' length 535044 bytes (522 KB) downloaded 522 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked package ‘cachem’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘cachem’ Warning: restored ‘cachem’ package ‘cli’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘cli’ Warning: restored ‘cli’ package ‘colorspace’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘colorspace’ Warning: restored ‘colorspace’ package ‘corrplot’ successfully unpacked and MD5 sums checked package ‘digest’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘digest’ Warning: restored ‘digest’ package ‘fansi’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘fansi’ Warning: restored ‘fansi’ package ‘farver’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘farver’ Warning: restored ‘farver’ package ‘fastmap’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘fastmap’ Warning: restored ‘fastmap’ package ‘fs’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘fs’ Warning: restored ‘fs’ package ‘gert’ successfully unpacked and MD5 sums checked package ‘glue’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘glue’ Warning: restored ‘glue’ package ‘gmp’ successfully unpacked and MD5 sums checked package ‘htmltools’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘htmltools’ Warning: restored ‘htmltools’ package ‘httpuv’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘httpuv’ Warning: restored ‘httpuv’ package ‘httr2’ successfully unpacked and MD5 sums checked package ‘insight’ successfully unpacked and MD5 sums checked package ‘minqa’ successfully unpacked and MD5 sums checked package ‘mvtnorm’ successfully unpacked and MD5 sums checked package ‘NMF’ successfully unpacked and MD5 sums checked package ‘openssl’ successfully unpacked and MD5 sums checked package ‘promises’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘promises’ Warning: restored ‘promises’ package ‘Rcpp’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘Rcpp’ Warning: restored ‘Rcpp’ package ‘RcppEigen’ successfully unpacked and MD5 sums checked package ‘rlang’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘rlang’ Warning: restored ‘rlang’ package ‘rmarkdown’ successfully unpacked and MD5 sums checked package ‘stringi’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘stringi’ Warning: restored ‘stringi’ package ‘vctrs’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘vctrs’ Warning: restored ‘vctrs’ package ‘waldo’ successfully unpacked and MD5 sums checked package ‘xfun’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in C:\Users\chaud\AppData\Local\Temp\RtmpkrYFpx\downloaded_packages installing the source packages ‘cpp11’, ‘curl’
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trying URL 'https://cran.rstudio.com/src/contrib/curl_5.2.2.tar.gz' Content type 'application/x-gzip' length 717715 bytes (700 KB) downloaded 700 KB
- installing source package 'cpp11' ... package 'cpp11' successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
- DONE (cpp11)
- installing source package 'curl' ... ** package 'curl' successfully unpacked and MD5 sums checked ERROR: cannot remove earlier installation, is it in use?
- removing 'C:/Users/chaud/AppData/Local/R/win-library/4.3/curl'
- restoring previous 'C:/Users/chaud/AppData/Local/R/win-library/4.3/curl' Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : problem copying C:\Users\chaud\AppData\Local\R\win-library\4.3\00LOCK-curl\curl\libs\x64\curl.dll to C:\Users\chaud\AppData\Local\R\win-library\4.3\curl\libs\x64\curl.dll: Permission denied
The downloaded source packages are in ‘C:\Users\chaud\AppData\Local\Temp\RtmpkrYFpx\downloaded_packages’ There were 18 warnings (use warnings() to see them)
snosna
Hello i am getting this weird error.
*Error in OncogenicPathways(maf, pathways = NULL, fontSize = 1, : could not find function "OncogenicPathways"
[sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Stockholm tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] ggpubr_0.6.0 ggplot2_3.5.1 tidyr_1.3.1 data.table_1.14.8 dplyr_1.1.3
[6] maftools_2.18.0
loaded via a namespace (and not attached): [1] gtable_0.3.5 htmlwidgets_1.6.4 devtools_2.4.5 remotes_2.5.0
[5] rstatix_0.7.2 lattice_0.21-8 vctrs_0.6.4 tools_4.3.1
[9] generics_0.1.3 curl_5.2.1 tibble_3.2.1 fansi_1.0.5
[13] pkgconfig_2.0.3 pheatmap_1.0.12 Matrix_1.6-4 RColorBrewer_1.1-3 [17] lifecycle_1.0.4 compiler_4.3.1 farver_2.1.1 stringr_1.5.1
[21] munsell_0.5.1 carData_3.0-5 httpuv_1.6.13 htmltools_0.5.7
[25] usethis_3.0.0 later_1.3.2 pillar_1.9.0 car_3.1-2
[29] urlchecker_1.0.1 ellipsis_0.3.2 cachem_1.0.8 sessioninfo_1.2.2
[33] abind_1.4-5 nlme_3.1-162 mime_0.12 tidyselect_1.2.1
[37] digest_0.6.33 stringi_1.7.12 purrr_1.0.2 labeling_0.4.3
[41] splines_4.3.1 fastmap_1.1.1 grid_4.3.1 colorspace_2.1-0
[45] cli_3.6.1 magrittr_2.0.3 survival_3.5-5 pkgbuild_1.4.4
[49] utf8_1.2.4 broom_1.0.6 withr_3.0.1 scales_1.3.0
[53] promises_1.2.1 backports_1.5.0 ggsignif_0.6.4 memoise_2.0.1
[57] DNAcopy_1.76.0 shiny_1.9.1 miniUI_0.1.1.1 mgcv_1.8-42
[61] profvis_0.3.8 rlang_1.1.2 Rcpp_1.0.11 xtable_1.8-4
[65] glue_1.6.2 BiocManager_1.30.24 pkgload_1.4.0 rstudioapi_0.16.0
[69] R6_2.5.1 fs_1.6.3 ](url)