I get the error in the title when I try to install the openCyto package or when I do a straight forward run of biocLite() with no arguments.
In the case of openCyto I get the message at the end after an appaently successful install of openCyto. Subsequently, "library(openCyto) fails ostensibly because it can't find flowClust()
Two questions:
1) Is the flowClust failure secondary to the filepath issue of biocLite() for boot, Matrix, and mgv and if so, how do I fix it?
2) What should I do to get openCyto to work properly?
Here is some context:
> ## try http:// if https:// URLs are not supported > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help > biocLite("openCyto") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing package(s) ‘openCyto’ also installing the dependency ‘flowClust’ Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘flowClust’ These will not be installed trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/openCyto_1.14.0.zip' Content type 'application/zip' length 3728048 bytes (3.6 MB) downloaded 3.6 MB package ‘openCyto’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\rbaer\AppData\Local\Temp\RtmpUlczKU\downloaded_packages installation path not writeable, unable to update packages: boot, Matrix, mgcv > library(openCyto) Error: package or namespace load failed for ‘openCyto’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘flowClust’
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A check with biocLite() suggests that I might be having a more general problem with install paths, but my .libPaths() seems to include a perfectly writable folder in my user folder. Any idea how to proceed in getting openCyto installed or better-state "usable".?
This seems like it should have an easy solution, but I could not find one in the FAQ. My local path has
> ## try http:// if https:// URLs are not supported > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help > biocLite() ## R version 3.0 or later BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). installation path not writeable, unable to update packages: boot, Matrix, mgcv > .libPaths() [1] "C:/Users/rbaer/Documents/R/win-library/3.4" [2] "C:/Program Files/R/R-3.4.1/library" > R.Version() $platform [1] "x86_64-w64-mingw32" $arch [1] "x86_64" $os [1] "mingw32" $system [1] "x86_64, mingw32" $status [1] "" $major [1] "3" $minor [1] "4.1" $year [1] "2017" $month [1] "06" $day [1] "30" $`svn rev` [1] "72865" $language [1] "R" $version.string [1] "R version 3.4.1 (2017-06-30)" $nickname [1] "Single Candle"
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Finally, sessionInfo() :
> sessionInfo() R version 3.4.1 (2017-06-30) 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 [7] base other attached packages: [1] flowWorkspace_3.24.4 ncdfFlow_2.22.2 [3] BH_1.65.0-1 RcppArmadillo_0.7.960.1.2 [5] flowCore_1.42.3 BiocInstaller_1.26.1 loaded via a namespace (and not attached): [1] lattice_0.20-35 pcaPP_1.9-72 colorspace_1.3-2 [4] stats4_3.4.1 RBGL_1.52.0 XML_3.98-1.9 [7] rlang_0.1.2 R.oo_1.21.0 hexbin_1.27.1 [10] glue_1.1.1 R.utils_2.5.0 Rgraphviz_2.20.0 [13] BiocGenerics_0.22.0 RColorBrewer_1.1-2 bindrcpp_0.2 [16] matrixStats_0.52.2 bindr_0.1 plyr_1.8.4 [19] robustbase_0.92-7 stringr_1.2.0 zlibbioc_1.22.0 [22] munsell_0.4.3 gtable_0.2.0 R.methodsS3_1.7.1 [25] mvtnorm_1.0-6 latticeExtra_0.6-28 Biobase_2.36.2 [28] parallel_3.4.1 DEoptimR_1.0-8 Rcpp_0.12.12 [31] KernSmooth_2.23-15 corpcor_1.6.9 scales_0.5.0 [34] graph_1.54.0 IDPmisc_1.1.17 gridExtra_2.3 [37] stringi_1.1.5 dplyr_0.7.3 clue_0.3-54 [40] grid_3.4.1 tools_3.4.1 magrittr_1.5 [43] tibble_1.3.4 cluster_2.0.6 rrcov_1.4-3 [46] pkgconfig_2.0.1 MASS_7.3-47 flowViz_1.40.0 [49] data.table_1.10.4 assertthat_0.2.0 R6_2.2.2 [52] compiler_3.4.1
Actually, the problem probably came about because someone ran R as Administrator. Better to always run R as a non-privileged user, correcting the previous installation by, e.g., starting over.