"R.version.3.4.0..2017.04.21."
"Platform: x86_64-apple-darwin15.6.0 (64-bit)"
"Running under: macOS Sierra 10.12.4"
"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_3.8.0"
"loaded via a namespace (and not attached):"
" [1] Rcpp_0.12.10       magrittr_1.5       splines_3.4.0     "
" [4] MASS_7.3-47        munsell_0.4.3      colorspace_1.3-2  "
" [7] lattice_0.20-35    minqa_1.2.4        stringr_1.2.0     "
"[10] plyr_1.8.4         caTools_1.17.1     tools_3.4.0       "
"[13] grid_3.4.0         gtable_0.2.0       nlme_3.1-131      "
"[16] KernSmooth_2.23-15 marray_1.54.0      gtools_3.5.0      "
"[19] survival_2.41-3    lme4_1.1-13        lazyeval_0.2.0    "
"[22] tibble_1.3.0       Matrix_1.2-10      reshape2_1.4.2    "
"[25] nloptr_1.0.4       ggplot2_2.2.1      bitops_1.0-6      "
"[28] ggrepel_0.6.5      stringi_1.1.5      limma_3.32.2      "
"[31] gdata_2.17.0       compiler_3.4.0     gplots_3.0.1      "
"[34] scales_0.4.1      "
" "
" "
"MSstats - dataProcess function"
" "
"The required input : provided - okay"
"summaryMethod : TMP"
"cutoffCensored : minFeature"
"censoredInt : NA"
"New input format : made new columns for analysis - okay"
"** There are31 intensities which are zero. These intensities are replaced with 1."
"Logarithm transformation: log2 transformation is done - okay"
"fillIncompleteRows = TRUE"
"*** Subject : 1, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 2, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 3, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Bare has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Eelgrass has multiple rows (duplicate rows) for some features ()"
"*** Subject : 1, Condition : Bare has multiple rows (duplicate rows) for some features ()"