system.file(file.path("Perl", script), package = "mosaics")
*no package 'mosaics2' exists on my system*. I tested this line:
system.file(file.path("Perl", script), package = "mosaics",mustWork=T)
and it works fine. Seems like a bug for my version of R/Bioconductor .... is there a mosaics2 package for an older Bioconductor?
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BiocInstaller_1.18.3 mosaics_2.2.0 Rcpp_0.11.6
loaded via a namespace (and not attached):
[1] MASS_7.3-40 IRanges_2.2.1 tools_3.2.0
[4] splines_3.2.0 S4Vectors_0.6.0 grid_3.2.0
[7] BiocGenerics_0.14.0 stats4_3.2.0 lattice_0.20-31
Jeremy Davis-Turak
> library(devtools)
> install('mosaics')
Installing mosaics
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.10.tar.gz'
Content type 'application/x-gzip' length 2446049 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
Installing Rcpp
'/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/bin/R' --no-site-file --no-environ \
--no-save --no-restore --quiet CMD INSTALL \
'/tmp/RtmpPSjG41/devtools4bcf5300c6d2/Rcpp' \
--library='/gpfs/home/fas/gerstein/jx98/R' --install-tests
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Date.cpp -o Date.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Module.cpp -o Module.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -I/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o
/gpfs/apps/hpc/Langs/GCC/4.8.2/bin/g++ -shared -L/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/lib -L/gpfs/apps/hpc/Libs/zlib/1.2.7/lib -L/gpfs/apps/hpc/Libs/bzip2/1.0.6/lib -L/gpfs/apps/hpc/Tools/XZ/5.0.7/lib -L/gpfs/apps/hpc/Tools/PCRE/8.40/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/gpfs/apps/hpc/Apps/R/3.3.2-generic/lib/R/lib -lR
installing to /gpfs/home/fas/gerstein/jx98/R/Rcpp/libs
** R
** inst
Warning in file.append(to[okay], from[okay]) :
write error during file append
Warning in file.append(to[okay], from[okay]) :
write error during file append
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in readRDS(nsInfoFilePath) : error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/gpfs/home/fas/gerstein/jx98/R/Rcpp’
* restoring previous ‘/gpfs/home/fas/gerstein/jx98/R/Rcpp’
Error: Command failed (1)
Jeremy Davis-Turak
Director of Bioinformatics
OnRamp BioInformatics, Inc.
Big Data Insights for BioInformatics
office/fax: (855) 7ONRAMP / (855) 766-7267 Extension 701
email: jer...@onramp.bio
web: www.onrampbioinformatics.com
♻︎ Please consider the environment before printing
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