also installing the dependencies 'bitops', 'fansi', 'gtools', 'caTools', 'plyr', 'glue', 'isoband', 'tibble', 'vctrs', 'purrr'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 0 != reported length 6802
2: In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/bitops_1.0-7.zip': HTTP status was '503 Service Unavailable'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'bitops' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip'
Content type 'application/zip' length 314168 bytes (306 KB)
===========================
downloaded 170 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 174878 != reported length 314168
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/fansi_1.0.6.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'fansi' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip'
Content type 'application/zip' length 362252 bytes (353 KB)
===================================
downloaded 247 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 253718 != reported length 362252
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/gtools_3.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'gtools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip'
Content type 'application/zip' length 246170 bytes (240 KB)
===================
downloaded 95 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 97498 != reported length 246170
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/caTools_1.18.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'caTools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip'
Content type 'application/zip' length 1154006 bytes (1.1 MB)
===========================
downloaded 624 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 639156 != reported length 1154006
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/plyr_1.8.9.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'plyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip'
Content type 'application/zip' length 160806 bytes (157 KB)
============================
downloaded 88 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 90198 != reported length 160806
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/glue_1.7.0.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'glue' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip'
Content type 'application/zip' length 1960578 bytes (1.9 MB)
=======================================
downloaded 1.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1556036 != reported length 1960578
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/isoband_0.2.7.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'isoband' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip'
Content type 'application/zip' length 689976 bytes (673 KB)
=============================
downloaded 397 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 407018 != reported length 689976
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tibble_3.2.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tibble' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip'
Content type 'application/zip' length 1339105 bytes (1.3 MB)
========================
downloaded 644 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 659596 != reported length 1339105
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/vctrs_0.6.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'vctrs' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip'
Content type 'application/zip' length 500075 bytes (488 KB)
==========================
downloaded 259 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 265398 != reported length 500075
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/purrr_1.0.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'purrr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gplots_3.1.3.1.zip'
Content type 'application/zip' length 604052 bytes (589 KB)
==================================================
downloaded 589 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip'
Content type 'application/zip' length 4528997 bytes (4.3 MB)
==================
downloaded 1.6 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1636336 != reported length 4528997
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/lme4_1.1-35.3.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'lme4' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape_0.8.9.zip'
Content type 'application/zip' length 170307 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip'
Content type 'application/zip' length 446505 bytes (436 KB)
====
downloaded 42 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 43478 != reported length 446505
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/reshape2_1.4.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'reshape2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip'
Content type 'application/zip' length 4820856 bytes (4.6 MB)
============================================
downloaded 4.1 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4321276 != reported length 4820856
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggplot2_3.5.0.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggplot2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip'
Content type 'application/zip' length 607986 bytes (593 KB)
======
downloaded 79 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 81438 != reported length 607986
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggrepel_0.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggrepel' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip'
Content type 'application/zip' length 2376172 bytes (2.3 MB)
==============
downloaded 675 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 691716 != reported length 2376172
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/data.table_1.15.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'data.table' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip'
Content type 'application/zip' length 1561579 bytes (1.5 MB)
=======================
downloaded 723 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 741356 != reported length 1561579
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/dplyr_1.1.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'dplyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip'
Content type 'application/zip' length 1267056 bytes (1.2 MB)
===================================
downloaded 872 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 893196 != reported length 1267056
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tidyr_1.3.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tidyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip'
Content type 'application/zip' length 6949342 bytes (6.6 MB)
======================
downloaded 3.0 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3122616 != reported length 6949342
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/survival_3.5-8.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'survival' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/doSNOW_1.0.20.zip'
Content type 'application/zip' length 29439 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip'
Content type 'application/zip' length 99079 bytes (96 KB)
=============================================
downloaded 88 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 90199 != reported length 99079
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/snow_0.4-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'snow' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/foreach_1.5.2.zip'
Content type 'application/zip' length 148277 bytes (144 KB)
==================================================
downloaded 144 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/stringr_1.5.1.zip'
Content type 'application/zip' length 318266 bytes (310 KB)
==================================================
downloaded 310 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip'
Content type 'application/zip' length 222198 bytes (216 KB)
================
downloaded 70 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 72678 != reported length 222198
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'randomForest' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip'
Content type 'application/zip' length 98247 bytes (95 KB)
==============
downloaded 28 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 28879 != reported length 98247
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'minpack.lm' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/optparse_1.7.5.zip'
Content type 'application/zip' length 83140 bytes (81 KB)
==================================================
downloaded 81 KB

package 'gplots' successfully unpacked and MD5 sums checked
package 'reshape' successfully unpacked and MD5 sums checked
package 'doSNOW' successfully unpacked and MD5 sums checked
package 'foreach' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'optparse' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Admin\AppData\Local\Temp\RtmpaiYeri\downloaded_packages
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31 ucrt)
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'lme4', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'RcppArmadillo',
  'rpart', 'spatial', 'survival', 'testthat'
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'MSstats' 


also installing the dependencies 'bitops', 'fansi', 'gtools', 'caTools', 'plyr', 'glue', 'isoband', 'tibble', 'vctrs', 'purrr'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 0 != reported length 6802
2: In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/bitops_1.0-7.zip': HTTP status was '503 Service Unavailable'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'bitops' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip'
Content type 'application/zip' length 314168 bytes (306 KB)
=============================
downloaded 179 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 183638 != reported length 314168
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/fansi_1.0.6.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'fansi' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip'
Content type 'application/zip' length 362252 bytes (353 KB)
==================================
downloaded 246 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 252258 != reported length 362252
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/gtools_3.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'gtools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip'
Content type 'application/zip' length 246170 bytes (240 KB)
====================
downloaded 99 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 101878 != reported length 246170
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/caTools_1.18.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'caTools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip'
Content type 'application/zip' length 1154006 bytes (1.1 MB)
============================
downloaded 637 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 652296 != reported length 1154006
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/plyr_1.8.9.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'plyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip'
Content type 'application/zip' length 160806 bytes (157 KB)
===============================
downloaded 99 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 101878 != reported length 160806
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/glue_1.7.0.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'glue' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip'
Content type 'application/zip' length 1960578 bytes (1.9 MB)
=======================================
downloaded 1.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1550196 != reported length 1960578
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/isoband_0.2.7.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'isoband' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip'
Content type 'application/zip' length 689976 bytes (673 KB)
================================
downloaded 434 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 444978 != reported length 689976
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tibble_3.2.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tibble' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip'
Content type 'application/zip' length 1339105 bytes (1.3 MB)
========================
downloaded 637 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 652296 != reported length 1339105
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/vctrs_0.6.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'vctrs' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip'
Content type 'application/zip' length 500075 bytes (488 KB)
===========================
downloaded 267 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 274158 != reported length 500075
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/purrr_1.0.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'purrr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gplots_3.1.3.1.zip'
Content type 'application/zip' length 604052 bytes (589 KB)
==================================================
downloaded 589 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip'
Content type 'application/zip' length 4528997 bytes (4.3 MB)
==================
downloaded 1.6 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1640716 != reported length 4528997
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/lme4_1.1-35.3.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'lme4' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape_0.8.9.zip'
Content type 'application/zip' length 170307 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip'
Content type 'application/zip' length 446505 bytes (436 KB)
====
downloaded 42 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 43478 != reported length 446505
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/reshape2_1.4.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'reshape2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip'
Content type 'application/zip' length 4820856 bytes (4.6 MB)
=================================
downloaded 3.1 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3261316 != reported length 4820856
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggplot2_3.5.0.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggplot2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip'
Content type 'application/zip' length 607986 bytes (593 KB)
========
downloaded 105 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 107718 != reported length 607986
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggrepel_0.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggrepel' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip'
Content type 'application/zip' length 2376172 bytes (2.3 MB)
==============
downloaded 658 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 674196 != reported length 2376172
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/data.table_1.15.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'data.table' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip'
Content type 'application/zip' length 1561579 bytes (1.5 MB)
=======================
downloaded 718 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 735516 != reported length 1561579
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/dplyr_1.1.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'dplyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip'
Content type 'application/zip' length 1267056 bytes (1.2 MB)
===================================
downloaded 867 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 888816 != reported length 1267056
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tidyr_1.3.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tidyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip'
Content type 'application/zip' length 6949342 bytes (6.6 MB)
============================
downloaded 3.8 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4020516 != reported length 6949342
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/survival_3.5-8.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'survival' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/doSNOW_1.0.20.zip'
Content type 'application/zip' length 29439 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip'
Content type 'application/zip' length 99079 bytes (96 KB)
=============================================
downloaded 88 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 90199 != reported length 99079
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/snow_0.4-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'snow' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/foreach_1.5.2.zip'
Content type 'application/zip' length 148277 bytes (144 KB)
==================================================
downloaded 144 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/stringr_1.5.1.zip'
Content type 'application/zip' length 318266 bytes (310 KB)
==================================================
downloaded 310 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip'
Content type 'application/zip' length 222198 bytes (216 KB)
================
downloaded 70 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 72678 != reported length 222198
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'randomForest' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip'
Content type 'application/zip' length 98247 bytes (95 KB)
==================
downloaded 35 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 36179 != reported length 98247
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'minpack.lm' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/optparse_1.7.5.zip'
Content type 'application/zip' length 83140 bytes (81 KB)
==================================================
downloaded 81 KB

package 'gplots' successfully unpacked and MD5 sums checked
package 'reshape' successfully unpacked and MD5 sums checked
package 'doSNOW' successfully unpacked and MD5 sums checked
package 'foreach' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'optparse' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Admin\AppData\Local\Temp\Rtmpm61qqK\downloaded_packages
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31 ucrt)
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'lme4', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'RcppArmadillo',
  'rpart', 'spatial', 'survival', 'testthat'
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'MSstats' 


also installing the dependencies 'bitops', 'fansi', 'gtools', 'caTools', 'plyr', 'glue', 'isoband', 'tibble', 'vctrs', 'purrr'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/bitops_1.0-7.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 0 != reported length 6802
2: In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/bitops_1.0-7.zip': HTTP status was '503 Service Unavailable'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'bitops' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip'
Content type 'application/zip' length 314168 bytes (306 KB)
============================
downloaded 172 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/fansi_1.0.6.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 176338 != reported length 314168
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/fansi_1.0.6.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'fansi' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip'
Content type 'application/zip' length 362252 bytes (353 KB)
===================================
downloaded 247 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gtools_3.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 253718 != reported length 362252
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/gtools_3.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'gtools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip'
Content type 'application/zip' length 246170 bytes (240 KB)
===================
downloaded 93 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/caTools_1.18.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 96038 != reported length 246170
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/caTools_1.18.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'caTools' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip'
Content type 'application/zip' length 1154006 bytes (1.1 MB)
============================
downloaded 634 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/plyr_1.8.9.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 649376 != reported length 1154006
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/plyr_1.8.9.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'plyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip'
Content type 'application/zip' length 160806 bytes (157 KB)
===========================
downloaded 86 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/glue_1.7.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 88738 != reported length 160806
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/glue_1.7.0.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'glue' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip'
Content type 'application/zip' length 1960578 bytes (1.9 MB)
=======================================
downloaded 1.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/isoband_0.2.7.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1560416 != reported length 1960578
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/isoband_0.2.7.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'isoband' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip'
Content type 'application/zip' length 689976 bytes (673 KB)
================================
downloaded 440 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tibble_3.2.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 450818 != reported length 689976
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tibble_3.2.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tibble' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip'
Content type 'application/zip' length 1339105 bytes (1.3 MB)
========================
downloaded 637 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/vctrs_0.6.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 652296 != reported length 1339105
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/vctrs_0.6.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'vctrs' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip'
Content type 'application/zip' length 500075 bytes (488 KB)
===========================
downloaded 269 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/purrr_1.0.2.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 275618 != reported length 500075
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/purrr_1.0.2.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'purrr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/gplots_3.1.3.1.zip'
Content type 'application/zip' length 604052 bytes (589 KB)
==================================================
downloaded 589 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip'
Content type 'application/zip' length 4528997 bytes (4.3 MB)
==================
downloaded 1.6 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/lme4_1.1-35.3.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1659696 != reported length 4528997
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/lme4_1.1-35.3.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'lme4' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape_0.8.9.zip'
Content type 'application/zip' length 170307 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip'
Content type 'application/zip' length 446505 bytes (436 KB)
===
downloaded 31 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/reshape2_1.4.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 31798 != reported length 446505
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/reshape2_1.4.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'reshape2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip'
Content type 'application/zip' length 4820856 bytes (4.6 MB)
=======================================
downloaded 3.6 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggplot2_3.5.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3820496 != reported length 4820856
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggplot2_3.5.0.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggplot2' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip'
Content type 'application/zip' length 607986 bytes (593 KB)
========
downloaded 102 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/ggrepel_0.9.5.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 104798 != reported length 607986
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/ggrepel_0.9.5.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'ggrepel' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip'
Content type 'application/zip' length 2376172 bytes (2.3 MB)
==============
downloaded 675 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/data.table_1.15.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 691716 != reported length 2376172
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/data.table_1.15.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'data.table' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip'
Content type 'application/zip' length 1561579 bytes (1.5 MB)
=======================
downloaded 718 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/dplyr_1.1.4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 735516 != reported length 1561579
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/dplyr_1.1.4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'dplyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip'
Content type 'application/zip' length 1267056 bytes (1.2 MB)
===================================
downloaded 866 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/tidyr_1.3.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 887356 != reported length 1267056
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/tidyr_1.3.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'tidyr' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip'
Content type 'application/zip' length 6949342 bytes (6.6 MB)
=====================
downloaded 2.9 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/survival_3.5-8.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3039396 != reported length 6949342
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/survival_3.5-8.zip': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'survival' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/doSNOW_1.0.20.zip'
Content type 'application/zip' length 29439 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip'
Content type 'application/zip' length 99079 bytes (96 KB)
============================================
downloaded 85 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/snow_0.4-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 87279 != reported length 99079
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/snow_0.4-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'snow' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/foreach_1.5.2.zip'
Content type 'application/zip' length 148277 bytes (144 KB)
==================================================
downloaded 144 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/stringr_1.5.1.zip'
Content type 'application/zip' length 318266 bytes (310 KB)
==================================================
downloaded 310 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip'
Content type 'application/zip' length 222198 bytes (216 KB)
================
downloaded 70 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 72678 != reported length 222198
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/randomForest_4.7-1.1.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'randomForest' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip'
Content type 'application/zip' length 98247 bytes (95 KB)
==========
downloaded 21 KB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://cran.us.r-project.org/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 21579 != reported length 98247
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/4.2/minpack.lm_1.2-4.zip': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'minpack.lm' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.2/optparse_1.7.5.zip'
Content type 'application/zip' length 83140 bytes (81 KB)
==================================================
downloaded 81 KB

package 'gplots' successfully unpacked and MD5 sums checked
package 'reshape' successfully unpacked and MD5 sums checked
package 'doSNOW' successfully unpacked and MD5 sums checked
package 'foreach' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'optparse' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Admin\AppData\Local\Temp\Rtmp0yeT1S\downloaded_packages
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31 ucrt)
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'lme4', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'RcppArmadillo',
  'rpart', 'spatial', 'survival', 'testthat'
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'MSstats'