Unable to download cytofkit

[rubikslucio]

Hi Guys, I am trying to install cytofkit in my windows 7. I inputed the command BiocManager::install("JinmiaoChenLab/cytofkit") but its not downloading the cytofkit package. Please help. Thanks. Here is the output code.

BiocManager::install("JinmiaoChenLab/cytofkit") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing github package(s) 'JinmiaoChenLab/cytofkit' Downloading GitHub repo JinmiaoChenLab/cytofkit@master checking for file 'C:\Users\ExpMedUser\AppData\Local\Temp\RtmpmUliSo\remotes171c3553484c\JinmiaoChenLab-cytofkit-c4f93e5/DESCRIPTION' ... checking for file 'C:\Users\ExpMedUser\AppData\Local\Temp\RtmpmUliSo\remotes171c3553484c\JinmiaoChenLab-cytofkit-c4f93e5/DESCRIPTION' ... √ checking for file 'C:\Users\ExpMedUser\AppData\Local\Temp\RtmpmUliSo\remotes171c3553484c\JinmiaoChenLab-cytofkit-c4f93e5/DESCRIPTION' (1.3s)

• preparing 'cytofkit': checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... √ checking DESCRIPTION meta-information
• cleaning src
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'cytofkit_1.11.3.tar.gz'
• installing source package 'cytofkit' ... libs ** arch - i386 C:/Program Files/Rtools/mingw_32/bin/g++ -I"E:/R-3.5.1/include" -DNDEBUG -I"E:/R-3.5.1/library/Rcpp/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Program: not found make: [RcppExports.o] Error 127 ERROR: compilation failed for package 'cytofkit'
• removing 'E:/R-3.5.1/library/cytofkit' In R CMD INSTALL Error in i.p(...) : (converted from warning) installation of package ‘C:/Users/EXPMED~1/AppData/Local/Temp/RtmpmUliSo/file171c4ed26d50/cytofkit_1.11.3.tar.gz’ had non-zero exit status In addition: Warning messages: 1: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers

Thanks.

[SamGG]

Hi, RTools is not installed at the default location. Install it at the root of the disk C:\, and the installation will finish. The current error is in fact C:/Program: not found. Because RTools is currently in the "C:/Program Files", the full command line "C:/Program Files/Rtools/mingw_32/bin/g++" has been split at the first space separator. So please install it at the root of your disk. HTH

[rubikslucio]

Hi SamGG,

Thank you for the help. I tried downloading Rtools using the command BiocManager::install("Rtools") this is the output.

BiocManager::install("Rtools") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) 'Rtools' Update old packages: 'processx' Update all/some/none? [a/s/n]: a There is a binary version available but the source version is later: binary source needs_compilation processx 3.2.0 3.2.1 TRUE Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/processx_3.2.0.zip' Content type 'application/zip' length 300367 bytes (293 KB) downloaded 293 KB package ‘processx’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\ExpMedUser\AppData\Local\Temp\RtmpeiMqCR\downloaded_packages Warning message: package ‘Rtools’ is not available (for R version 3.5.1)

Is there a different way to save the Rtools in my C drive then the one I am trying? Thanks for the help.

[SamGG]

Hi. Rtools is not a package of R. Rtools is a program. It must be install apart from R or RStudio. It brings tools to R, tools to build packages. You will find Rtools at . Since Rtools is already installed in your computer, I thought you did it. Please uninstall the current Rtools from your computer, restart your computer, then install Rtools as administrator, using default proposals but adding Rtools to the PATH variable. I did it on many computers of trainees and this procedure works. Best

[rubikslucio]

Hi SamGG,

Thank you so much for the help it worked. Best

[SamGG]

I am glad you succeeded. Please, close this issue if you feel it is solved. Enjoy cytofkit.