I am trying to install the flowViz package and it is saying that the dependency flowCore is not available even though it has just installed it.
I created a new directory, set the .libPaths() to point only to there and then called
in the usual fashion. This installs all of the necessary dependencies - including flowCore - and then when it gets to flowViz itself it says flowCore is not found. The tail end of the output is below:
** R ** data ** 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 * DONE (flowCore) * installing *source* package ‘flowViz’ ... ** 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 Error : package ‘flowCore’ required by ‘flowViz’ could not be found Error: loading failed Execution halted ERROR: loading failed * removing ‘/home/Foo/Bar/flowViz’
The downloaded source packages are in ‘/tmp/RtmpiDqYYK/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘flowViz’ had non-zero exit status Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
I can even load flowCore after that:
> > library(flowCore) > > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS
Matrix products: default BLAS: /Foo/R-3.5.1/lib/R/lib/libRblas.so LAPACK: /Foo/R-3.5.1/lib/R/lib/libRlapack.so
locale:  LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8 LC_MONETARY=en_NZ.UTF-8  LC_MESSAGES=en_NZ.UTF-8 LC_PAPER=en_NZ.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
attached base packages:  stats graphics grDevices utils datasets methods base
other attached packages:  flowCore_1.46.1 BiocInstaller_1.30.0 prettycode_1.0.1
loaded via a namespace (and not attached):  Rcpp_0.12.18 mvtnorm_1.0-8 lattice_0.20-35 matrixStats_0.54.0 corpcor_1.6.9 digest_0.6.16 crayon_1.3.4  withr_2.1.2 rrcov_1.4-4 grid_3.5.1 pcaPP_1.9-73 stats4_3.5.1 graph_1.58.0 robustbase_0.93-2  devtools_1.13.6 tools_3.5.1 Biobase_2.40.0 DEoptimR_1.0-8 parallel_3.5.1 compiler_3.5.1 BiocGenerics_0.26.0  cluster_2.0.7-1 memoise_1.1.0
And yet flowViz still says it cannot be found.
I have recently upgraded to R 3.5.1 and I suspect the error is related to this rather than Bioconductor, however I haven't found any CRAN packages that produce a similar error.
I got the same results trying to install RBGL from Bioconductor where it installed the graph package and then said RBGL can't be installed because graph cannot be found.
I'm using Bioconductor 3.7.
Any help would be much appreciated,