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nereidaramirez
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@nereidaramirez-15929
Last seen 7.4 years ago
Yesterday I was walking through this tutorial and I was able to run every package, but when I tried to execute the script today I wasn't able to load libraries that I had already installed (e.g. BiocStyle and GenomicFeatures). The error that I keep getting is attached below. Thus far I've tried every suggestion on this thread but nothing has worked. Is there anyway to restore these packages in R 3.5.0?
> install.packages("BiocStyle", repos="https://bioconductor.org/biocLite.R", dependencies=TRUE)
Installing package into ‘C:/Users/KimLab/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
unable to access index for repository https://bioconductor.org/biocLite.R/src/contrib:
cannot open URL 'https://bioconductor.org/biocLite.R/src/contrib/PACKAGES'
Warning in install.packages :
package ‘BiocStyle’ is not available (for R version 3.5.0)
Warning in install.packages :
unable to access index for repository https://bioconductor.org/biocLite.R/bin/windows/contrib/3.5:
cannot open URL 'https://bioconductor.org/biocLite.R/bin/windows/contrib/3.5/PACKAGES'
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.30.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 locfit_1.5-9.1
[3] lattice_0.20-35 assertthat_0.2.0
[5] digest_0.6.15 SingleCellExperiment_1.2.0
[7] mime_0.5 R6_2.2.2
[9] GenomeInfoDb_1.16.0 plyr_1.8.4
[11] stats4_3.5.0 ggplot2_2.2.1
[13] pillar_1.2.3 zlibbioc_1.26.0
[15] rlang_0.2.0 lazyeval_0.2.1
[17] data.table_1.11.2 S4Vectors_0.18.2
[19] Matrix_1.2-14 BiocParallel_1.14.1
[21] RCurl_1.95-4.10 munsell_0.4.3
[23] shiny_1.1.0 DelayedArray_0.6.0
[25] compiler_3.5.0 httpuv_1.4.3
[27] vipor_0.4.5 pkgconfig_2.0.1
[29] BiocGenerics_0.26.0 ggbeeswarm_0.6.0
[31] htmltools_0.3.6 tidyselect_0.2.4
[33] SummarizedExperiment_1.10.1 tibble_1.4.2
[35] gridExtra_2.3 GenomeInfoDbData_1.1.0
[37] edgeR_3.22.2 IRanges_2.14.10
[39] matrixStats_0.53.1 viridisLite_0.3.0
[41] dplyr_0.7.5 later_0.7.2
[43] bitops_1.0-6 grid_3.5.0
[45] xtable_1.8-2 gtable_0.2.0
[47] magrittr_1.5 scales_0.5.0
[49] XVector_0.20.0 viridis_0.5.1
[51] promises_1.0.1 bindrcpp_0.2.2
[53] limma_3.36.1 DelayedMatrixStats_1.2.0
[55] tools_3.5.0 Biobase_2.40.0
[57] glue_1.2.0 beeswarm_0.2.3
[59] purrr_0.2.4 parallel_3.5.0
[61] yaml_2.1.19 colorspace_1.3-2
[63] GenomicRanges_1.32.3 shinydashboard_0.7.0
[65] bindr_0.1.1
Yes I do still get errors:
> BiocInstaller::biocLite('BiocStyle') BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘BiocStyle’ trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocStyle_2.8.1.zip' Content type 'application/zip' length 754238 bytes (736 KB) downloaded 736 KB package ‘BiocStyle’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages installation path not writeable, unable to update packages: MASS, survival Old packages: 'data.table', 'openxlsx', 'rrcov', 'simpleSingleCell', 'utf8' Update all/some/none? [a/s/n]: a also installing the dependency ‘zip’ There are binary versions available but the source versions are later: binary source needs_compilation data.table 1.11.2 1.11.4 TRUE openxlsx 4.0.17 4.1.0 TRUE Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/zip_1.0.0.zip' Content type 'application/zip' length 104827 bytes (102 KB) downloaded 102 KB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/data.table_1.11.2.zip' Content type 'application/zip' length 1825285 bytes (1.7 MB) downloaded 1.7 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/openxlsx_4.0.17.zip' Content type 'application/zip' length 2427142 bytes (2.3 MB) downloaded 2.3 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rrcov_1.4-4.zip' Content type 'application/zip' length 1662044 bytes (1.6 MB) downloaded 1.6 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/utf8_1.1.4.zip' Content type 'application/zip' length 214628 bytes (209 KB) downloaded 209 KB package ‘zip’ successfully unpacked and MD5 sums checked package ‘data.table’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘data.table’ package ‘openxlsx’ successfully unpacked and MD5 sums checked package ‘rrcov’ successfully unpacked and MD5 sums checked package ‘utf8’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages installing the source package ‘simpleSingleCell’ trying URL 'https://bioconductor.org/packages/3.7/workflows/src/contrib/simpleSingleCell_1.2.1.tar.gz' Content type 'application/x-gzip' length 16035226 bytes (15.3 MB) downloaded 15.3 MB * installing *source* package 'simpleSingleCell' ... ** inst ** help No man pages found in package 'simpleSingleCell' *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded *** arch - i386 Error: package or namespace load failed for 'BiocStyle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'stringi' Error : package 'BiocStyle' could not be loaded Error: loading failed Execution halted *** arch - x64 Error: package or namespace load failed for 'BiocStyle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'stringi' Error : package 'BiocStyle' could not be loaded Error: loading failed Execution halted ERROR: loading failed for 'i386', 'x64' * removing 'C:/Users/KimLab/Documents/R/win-library/3.5/simpleSingleCell' * restoring previous 'C:/Users/KimLab/Documents/R/win-library/3.5/simpleSingleCell' In R CMD INSTALL The downloaded source packages are in ‘C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘simpleSingleCell’ had non-zero exit statusInstall the missing dependency
BiocInstaller::biocLite("stringi"); it's not really clear why stringi is (no longer) installed.