Entering edit mode
VictoriaL
•
0
@victorial-22345
Last seen 3.2 years 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
