Installing packages into 'C:/Users/nicksh/Documents/R/win-library/4.1'
(as 'lib' is unspecified)
also installing the dependencies 'cli', 'rlang', 'vctrs'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/cli_3.3.0.zip'
Content type 'application/zip' length 1259629 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/rlang_1.0.4.zip'
Content type 'application/zip' length 1758719 bytes (1.7 MB)
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downloaded 1.7 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/vctrs_0.4.1.zip'
Content type 'application/zip' length 1571666 bytes (1.5 MB)
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downloaded 1.5 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/gplots_3.1.3.zip'
Content type 'application/zip' length 603572 bytes (589 KB)
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downloaded 589 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/lme4_1.1-30.zip'
Content type 'application/zip' length 5367701 bytes (5.1 MB)
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downloaded 5.1 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/reshape_0.8.9.zip'
Content type 'application/zip' length 170401 bytes (166 KB)
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downloaded 166 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/reshape2_1.4.4.zip'
Content type 'application/zip' length 817963 bytes (798 KB)
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downloaded 798 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/ggplot2_3.3.6.zip'
Content type 'application/zip' length 4127372 bytes (3.9 MB)
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downloaded 3.9 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/ggrepel_0.9.1.zip'
Content type 'application/zip' length 1119272 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/data.table_1.14.2.zip'
Content type 'application/zip' length 2600424 bytes (2.5 MB)
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downloaded 2.5 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/dplyr_1.0.9.zip'
Content type 'application/zip' length 1392274 bytes (1.3 MB)
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downloaded 1.3 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/tidyr_1.2.0.zip'
Content type 'application/zip' length 1115165 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/survival_3.3-1.zip'
Content type 'application/zip' length 6965734 bytes (6.6 MB)
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downloaded 6.6 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/doSNOW_1.0.20.zip'
Content type 'application/zip' length 29316 bytes (28 KB)
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downloaded 28 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/snow_0.4-4.zip'
Content type 'application/zip' length 99111 bytes (96 KB)
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downloaded 96 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/foreach_1.5.2.zip'
Content type 'application/zip' length 148214 bytes (144 KB)
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downloaded 144 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/stringr_1.4.0.zip'
Content type 'application/zip' length 216721 bytes (211 KB)
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downloaded 211 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/randomForest_4.7-1.1.zip'
Content type 'application/zip' length 252324 bytes (246 KB)
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downloaded 246 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/minpack.lm_1.2-2.zip'
Content type 'application/zip' length 123270 bytes (120 KB)
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downloaded 120 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/optparse_1.7.3.zip'
Content type 'application/zip' length 83111 bytes (81 KB)
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downloaded 81 KB

package 'cli' successfully unpacked and MD5 sums checked
package 'rlang' successfully unpacked and MD5 sums checked
package 'vctrs' successfully unpacked and MD5 sums checked
package 'gplots' successfully unpacked and MD5 sums checked
package 'lme4' successfully unpacked and MD5 sums checked
package 'reshape' successfully unpacked and MD5 sums checked
package 'reshape2' successfully unpacked and MD5 sums checked
package 'ggplot2' successfully unpacked and MD5 sums checked
package 'ggrepel' successfully unpacked and MD5 sums checked
package 'data.table' successfully unpacked and MD5 sums checked
package 'dplyr' successfully unpacked and MD5 sums checked
package 'tidyr' successfully unpacked and MD5 sums checked
package 'survival' successfully unpacked and MD5 sums checked
package 'doSNOW' successfully unpacked and MD5 sums checked
package 'snow' successfully unpacked and MD5 sums checked
package 'foreach' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'randomForest' successfully unpacked and MD5 sums checked
package 'minpack.lm' successfully unpacked and MD5 sums checked
package 'optparse' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\nicksh\AppData\Local\Temp\RtmpSeIy4J\downloaded_packages
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'MSstats'

  There is a binary version available but the source version is later:
        binary source needs_compilation
MSstats  4.1.1  4.2.0              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/MSstats_4.1.1.zip'
Content type 'application/zip' length 1620557 bytes (1.5 MB)
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downloaded 1.5 MB

package 'MSstats' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\nicksh\AppData\Local\Temp\RtmpSeIy4J\downloaded_packages
Old packages: 'MSstats', 'BiocManager', 'checkmate', 'class', 'cli', 'cluster',
  'colorspace', 'crayon', 'doSNOW', 'dplyr', 'fansi', 'farver', 'foreach',
  'foreign', 'generics', 'ggplot2', 'glue', 'gplots', 'gtools', 'iterators',
  'limma', 'lme4', 'magrittr', 'MASS', 'Matrix', 'mgcv', 'minpack.lm',
  'MSstatsConvert', 'nlme', 'nloptr', 'nnet', 'optparse', 'pillar', 'plyr',
  'randomForest', 'RColorBrewer', 'Rcpp', 'RcppArmadillo', 'RcppEigen',
  'reshape', 'rlang', 'rpart', 'scales', 'spatial', 'stringi', 'survival',
  'tibble', 'tidyr', 'tidyselect', 'vctrs', 'withr'