installing GO.bd for WGCNA
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0
Entering edit mode
VictoriaL • 0
@victorial-22345
Last seen 7 months ago

I have having problems installing my WGCNA and GO.db. I had to re-install my R studio and now unable to install my WGCNA and GO.db programmes.

if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("GO.db") 


Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GO.db_3.12.1.tar.gz'
Content type 'application/x-gzip' length 31330588 bytes (29.9 MB)
downloaded 29.9 MB

'"C:\PROGRA~1\R\R-40~1.2/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
    ‘C:\Users\victo\AppData\Local\Temp\Rtmp0IsCwi\downloaded_packages’
Installation path not writeable, unable to update packages: codetools, KernSmooth, MASS, mgcv, nlme, survival
Old packages: 'backports', 'broom', 'pkgbuild', 'rmarkdown', 'tinytex'
Update all/some/none? [a/s/n]: install.packages(c("dynamicTreeCut", "cluster", "flashClust", "Hmisc", "reshape", "foreach", "doParallel") ) 
Update all/some/none? [a/s/n]: source("http://bioconductor.org/biocLite.R") 
Update all/some/none? [a/s/n]: biocLite("impute")
Update all/some/none? [a/s/n]: install.packages("WGCNA")
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
          binary source needs_compilation
backports  1.2.0  1.2.1              TRUE
broom      0.7.2  0.7.3             FALSE
pkgbuild   1.1.0  1.2.0             FALSE
rmarkdown    2.5    2.6             FALSE
tinytex     0.27   0.28             FALSE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.2.0.zip'
Content type 'application/zip' length 98138 bytes (95 KB)
downloaded 95 KB

package ‘backports’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\victo\AppData\Local\Temp\Rtmp0IsCwi\downloaded_packages
installing the source packages ‘broom’, ‘pkgbuild’, ‘rmarkdown’, ‘tinytex’

trying URL 'https://cran.rstudio.com/src/contrib/broom_0.7.3.tar.gz'
Content type 'application/x-gzip' length 618499 bytes (604 KB)
downloaded 604 KB

trying URL 'https://cran.rstudio.com/src/contrib/pkgbuild_1.2.0.tar.gz'
Content type 'application/x-gzip' length 30383 bytes (29 KB)
downloaded 29 KB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.6.tar.gz'
Content type 'application/x-gzip' length 3213194 bytes (3.1 MB)
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/tinytex_0.28.tar.gz'
Content type 'application/x-gzip' length 27595 bytes (26 KB)
downloaded 26 KB

'"C:\PROGRA~1\R\R-40~1.2/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.
'"C:\PROGRA~1\R\R-40~1.2/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.
'"C:\PROGRA~1\R\R-40~1.2/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.
'"C:\PROGRA~1\R\R-40~1.2/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
    ‘C:\Users\victo\AppData\Local\Temp\Rtmp0IsCwi\downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘GO.db’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘broom’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘pkgbuild’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘tinytex’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘rmarkdown’ had non-zero exit status
GO.db WGCNA • 242 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

I think you should be able to install binaries that don't contain compiled code on a Windows box that doesn't have Rtools installed, but maybe not? Anyway, installing Rtools should update your path at the very least, so go here and get the installer.

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