I'm having trouble installing RforProteomics after the other dependencies have been installed. I think the problem is related to unzipping and then loading the library. I wanted to report this because of the error message I received. However, if anyone has ideas on how to solve the problem I'd be very receptive to that as well.
mzR has been built against a different Rcpp version (0.12.1) than is installed on your system (0.12.3). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc support forum...
Warning messages: 1: running command '"C:/Users/path" CMD INSTALL -l "C:/Users/path/library" C:/Users/path/synapterdata_1.8.0.tar.gz' had status 1 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘synapterdata’ had non-zero exit status 3: running command '"C:/Users/path/R" CMD INSTALL -l "C:/Users/path/library" C:/Users/path/RforProteomics_1.8.0.tar.gz' had status 1 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RforProteomics’ had non-zero exit status
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  msdata_0.8.0 BiocInstaller_1.20.1 hpar_1.12.0 rols_1.12.1 pRolocdata_1.8.0 cluster_2.0.3 annotate_1.48.0  XML_3.98-1.4 AnnotationDbi_1.32.3 IRanges_2.4.8 S4Vectors_0.8.11 rpx_1.6.0 MSnbase_1.18.1 ProtGenerics_1.2.1  BiocParallel_1.4.3 Biobase_2.30.0 BiocGenerics_0.16.1 MSnID_1.4.0 mzID_1.8.0 mzR_2.4.0 Rcpp_0.12.3 loaded via a namespace (and not attached):  SSOAP_0.8-0 rda_1.0.2-2 magrittr_1.5 fpc_2.1-10 MASS_7.3-45 sfsmisc_1.1-0 zlibbioc_1.16.0  mclust_5.1 R.cache_0.12.0 xtable_1.8-2 colorspace_1.2-6 impute_1.44.0 lattice_0.20-33 R6_2.1.2  foreach_1.4.3 R.oo_1.20.0 futile.logger_1.4.1 lambda.r_1.1.7 class_7.3-14 ggvis_0.4.2 iterators_1.0.8  htmltools_0.3 modeltools_0.2-21 assertthat_0.1 digest_0.6.9 preprocessCore_1.32.0 shiny_0.13.1 RCurl_1.95-4.8  limma_3.26.8 DEoptimR_1.0-4 threejs_0.2.1 scales_0.4.0 pls_2.5-0 pcaMethods_1.60.0 R.methodsS3_1.7.1  diptest_0.75-7 httpuv_1.3.3 flexmix_2.3-13 munsell_0.4.3 doParallel_1.0.10 XMLSchema_0.7-2 plyr_1.8.3  dplyr_0.4.3 stringr_1.0.0 prabclus_2.2-6 tools_3.2.3 grid_3.2.3 nnet_7.3-12 data.table_1.9.6  gtable_0.2.0 affy_1.48.0 DBI_0.3.1 affyio_1.40.0 kernlab_0.9-23 trimcluster_0.1-2 ggplot2_2.1.0  reshape2_1.4.1 htmlwidgets_0.6 base64enc_0.1-3 bitops_1.0-6 R.utils_2.2.0 codetools_0.2-14 futile.options_1.0.0  rpart_4.1-10 MALDIquant_1.14 robustbase_0.92-5 RSQLite_1.0.0 mime_0.4 mlbench_2.1-1 stringi_1.0-1  mvtnorm_1.0-5 vsn_3.38.0 chron_2.3-47