"R.version.3.4.0..2017.04.21."
"Platform: x86_64-apple-darwin15.6.0 (64-bit)"
"Running under: OS X El Capitan 10.11.6"
"Matrix products: default"
"BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib"
"LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib"
"locale:"
"[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
"attached base packages:"
"[1] stats     graphics  grDevices utils     datasets  methods   base     "
"other attached packages:"
"[1] MSstats_3.8.2        BiocInstaller_1.26.0"
"loaded via a namespace (and not attached):"
" [1] Rcpp_0.12.11          nloptr_1.0.4          compiler_3.4.0        plyr_1.8.4            bitops_1.0-6         "
" [6] ProtGenerics_1.8.0    iterators_1.0.8       tools_3.4.0           zlibbioc_1.22.0       MALDIquant_1.16.2    "
"[11] digest_0.6.12         lme4_1.1-13           preprocessCore_1.38.1 tibble_1.3.3          gtable_0.2.0         "
"[16] nlme_3.1-131          lattice_0.20-35       rlang_0.1.1           Matrix_1.2-10         foreach_1.4.3        "
"[21] ggrepel_0.6.5         parallel_3.4.0        stringr_1.2.0         caTools_1.17.1        gtools_3.5.0         "
"[26] S4Vectors_0.14.3      IRanges_2.10.2        stats4_3.4.0          grid_3.4.0            Biobase_2.36.2       "
"[31] impute_1.50.1         marray_1.54.0         survival_2.41-3       XML_3.98-1.9          BiocParallel_1.10.1  "
"[36] minpack.lm_1.2-1      gdata_2.18.0          minqa_1.2.4           limma_3.32.2          magrittr_1.5         "
"[41] reshape2_1.4.2        ggplot2_2.2.1         mzR_2.10.0            gplots_3.0.1          scales_0.4.1         "
"[46] pcaMethods_1.68.0     codetools_0.2-15      BiocGenerics_0.22.0   splines_3.4.0         MASS_7.3-47          "
"[51] mzID_1.14.0           MSnbase_2.2.0         colorspace_1.3-2      KernSmooth_2.23-15    stringi_1.1.5        "
"[56] affy_1.54.0           lazyeval_0.2.0        munsell_0.4.3         doParallel_1.0.10     vsn_3.44.0           "
"[61] affyio_1.46.0        "
" "
" "
"MSstats - dataProcess function"
" "
"The required input : provided - okay"
"summaryMethod : TMP"
"cutoffCensored : minFeature"
"censoredInt : NA"
"New input format : made new columns for analysis - okay"
"** There are1295 intensities which are zero. These intensities are replaced with 1."
"Logarithm transformation: log2 transformation is done - okay"