unable to install scGate or ProjecTILs libraries

[ashkanshahbandi]

Hi, I have been trying to install these libraries into R-Studio, but I keep getting the following errors:

remotes::install_github("carmonalab/scGate") Downloading GitHub repo carmonalab/scGate@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: stringi (1.7.6 -> 1.7.8) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 stringi (1.7.6 -> 1.7.8) [CRAN] Skipping 1 packages not available: UCell Installing 2 packages: stringi, UCell Installing packages into ‘C:/Users/ashka/Documents/renv/library/R-4.1/x86_64-w64-mingw32’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation stringi 1.7.6 1.7.8 TRUE

Binaries will be installed trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.1/stringi_1.7.6.zip' Content type 'application/zip' length 16449819 bytes (15.7 MB) downloaded 15.7 MB

package ‘stringi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\ashka\AppData\Local\Temp\Rtmpc50GBN\downloaded_packages Running R CMD build...

• checking for file 'C:\Users\ashka\AppData\Local\Temp\Rtmpc50GBN\remotes73b047e96ee2\carmonalab-scGate-1b23084/DESCRIPTION' ... OK
• preparing 'scGate':
• checking DESCRIPTION meta-information ... OK
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'scGate_1.2.0.tar.gz' Installing package into ‘C:/Users/ashka/Documents/renv/library/R-4.1/x86_64-w64-mingw32’ (as ‘lib’ is unspecified) ERROR: dependency 'UCell' is not available for package 'scGate'
• removing 'C:/Users/ashka/Documents/renv/library/R-4.1/x86_64-w64-mingw32/scGate' Warning messages: 1: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 3: package ‘UCell’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 4: In i.p(...) : installation of package ‘C:/Users/ashka/AppData/Local/Temp/Rtmpc50GBN/file73b0491424d0/scGate_1.2.0.tar.gz’ had non-zero exit status

remotes::install_github("carmonalab/ProjecTILs") Downloading GitHub repo carmonalab/ProjecTILs@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: stringi (1.7.6 -> 1.7.8) [CRAN]

Enter one or more numbers, or an empty line to skip updates: Running R CMD build...

• checking for file 'C:\Users\ashka\AppData\Local\Temp\Rtmpc50GBN\remotes73b014782336\carmonalab-ProjecTILs-370abd8/DESCRIPTION' ... OK
• preparing 'ProjecTILs':
• checking DESCRIPTION meta-information ... OK
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'ProjecTILs_3.0.0.tar.gz' Installing package into ‘C:/Users/ashka/Documents/renv/library/R-4.1/x86_64-w64-mingw32’ (as ‘lib’ is unspecified) ERROR: dependencies 'UCell', 'scGate' are not available for package 'ProjecTILs'
• removing 'C:/Users/ashka/Documents/renv/library/R-4.1/x86_64-w64-mingw32/ProjecTILs' Warning messages: 1: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 3: In i.p(...) : installation of package ‘C:/Users/ashka/AppData/Local/Temp/Rtmpc50GBN/file73b07ff54eff/ProjecTILs_3.0.0.tar.gz’ had non-zero exit status

I have been able to successfully install the packages on another computer a few months ago, so I'm not sure what the problem is now. Can someone help me with this? Thanks!

[mass-a]

Hello, I can see from your log:

Skipping 1 packages not available: UCell

What version of R and Bioconductor are you using? Note that UCell is available from Bioconductor starting from Bioc-3.15 (R-4.2).

If you are using R<=4.1 you should install an older version of UCell from the github repo:

library(remotes)
remotes::install_github("carmonalab/UCell", ref="v1.3")

Similarly, scGate should be installed from github:

remotes::install_github("carmonalab/scGate")

Best -m

[ashkanshahbandi]

Hello, I can see from your log:

Skipping 1 packages not available: UCell

What version of R and Bioconductor are you using? Note that UCell is available from Bioconductor starting from Bioc-3.15 (R-4.2).

If you are using R<=4.1 you should install an older version of UCell from the github repo:

library(remotes)
remotes::install_github("carmonalab/UCell", ref="v1.3")

Similarly, scGate should be installed from github:

remotes::install_github("carmonalab/scGate")

Best -m

Hi, I am using R.4.2.1

I installed scGate from github but I am now getting the following errors:

remotes::install_github("carmonalab/scGate") Downloading GitHub repo carmonalab/scGate@HEAD Installing 1 packages: GenomeInfoDbData Installing package into ‘C:/Users/ashka/Documents/renv/library/R-4.2/x86_64-w64-mingw32’ (as ‘lib’ is unspecified) installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz' Content type 'application/x-gzip' length 11512907 bytes (11.0 MB) downloaded 11.0 MB

• installing source package 'GenomeInfoDbData' ... using staged installation data inst help * installing help indices building package indices Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'renv/activate.R': No such file or directory Execution halted ERROR: installing package indices failed
• removing 'C:/Users/ashka/Documents/renv/library/R-4.2/x86_64-w64-mingw32/GenomeInfoDbData'

The downloaded source packages are in ‘C:\Users\ashka\AppData\Local\Temp\RtmpwpIrnt\downloaded_packages’ Running R CMD build...

• checking for file 'C:\Users\ashka\AppData\Local\Temp\RtmpwpIrnt\remotes436879ff78e2\carmonalab-scGate-1b23084/DESCRIPTION' ... OK
• preparing 'scGate':
• checking DESCRIPTION meta-information ... OK
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'scGate_1.2.0.tar.gz' Installing package into ‘C:/Users/ashka/Documents/renv/library/R-4.2/x86_64-w64-mingw32’ (as ‘lib’ is unspecified)
• installing source package 'scGate' ... using staged installation R ** data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'renv/activate.R': No such file or directory Execution halted ERROR: lazy loading failed for package 'scGate'
• removing 'C:/Users/ashka/Documents/renv/library/R-4.2/x86_64-w64-mingw32/scGate' Warning messages: 1: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers 3: In i.p(...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status 4: In i.p(...) : installation of package ‘C:/Users/ashka/AppData/Local/Temp/RtmpwpIrnt/file43687e8c501d/scGate_1.2.0.tar.gz’ had non-zero exit status

[mass-a]

Now your log says that the installation of the GenomeInfoDbData package is failing. Perhaps try to install that package manually? In any case I am not sure why it's being installed, since it is not a dependency of scGate. You also have warnings from renv, so perhaps you have to check if you set up your R project correctly.