Unable to install MSnbase

[cdlawless]

Running through Rstudio on Ubuntu 16.04 with R v3.4.2

> biocLite("MSnbase")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘MSnbase’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/MSnbase_2.4.0.tar.gz'
Content type 'application/x-gzip' length 4668336 bytes (4.5 MB)
==================================================
downloaded 4.5 MB

* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG  -I"/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum1_class.c -o Spectrum1_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum2_class.c -o Spectrum2_class.o
g++  -I/usr/share/R/include -DNDEBUG  -I"/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/usr/lib/R/lib -lR
installing to /home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘MSnbase’ is not available and has been replaced
by .GlobalEnv when processing object ‘itraqdata’
Warning: namespace ‘MSnbase’ is not available and has been replaced
by .GlobalEnv when processing object ‘itraqdata’
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘scales’
ERROR: lazy loading failed for package ‘MSnbase’
* removing ‘/home/mjfidcl2/R/x86_64-pc-linux-gnu-library/3.4/MSnbase’

The downloaded source packages are in
	‘/tmp/RtmplvZUtR/downloaded_packages’
installation path not writeable, unable to update packages: codetools, lattice, mgcv, spatial
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘MSnbase’ had non-zero exit status

Any help appreciated.

Craig

[lgatto]

Could you first install scales and try again. If that fixes it, could you let me know here and I will add it as a explicit dependency to avoid this error in the future. Thanks.

[cdlawless]

Hi Laurent,
Had to install scales, lazyeval and tibble to get it working.
Thank you.

[lgatto]

This is a bit weird... I'm wondering of some dependencies haven't declared their properly. I'll try to find out. Thank you.