Install the xMWAS package for mac user need several packages installed manually

[jamesjiadazhan]

Hi,

I encountered a significant issue while downloading the xMWAS from GitHub. This may be related to the fact that I am using Mac and my RStudio is very updated: RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_3_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36

I spent a lot of time fixing it by installing several packages by myself ahead in order to make the xMWAS downloading work without problem. Below are my codes:

install.packages("devtools",repos="http://cran.r-project.org")
BiocManager::install("graph")
BiocManager::install("RBGL")
BiocManager::install("AnnotationDbi")
BiocManager::install("GO.db")
BiocManager::install("preprocessCore")
BiocManager::install("impute")

devtools::install_github("kuppal2/xMWAS")

Generally, I think the problems are that the xMWAS package relies on other packages to have the most recent version available, but the internal functions in the xMWAS for downloading other packages are not working well at least for my situation. The internal functions did not work as shown below. 1/2/3/4 didn't work for the (Which would you like to update), and Yes/no/cancel didn't work for (the Do you want to install from sources the package which needs compilation).

Which would you like to update?

1: All                         
2: CRAN packages only          
3: None                        
4: fields (14.0 -> 14.1) [CRAN] 

Enter one or more numbers, or an empty line to skip updates:

There is a binary version available but the source version is later:
       binary source needs_compilation
fields   14.0   14.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

Below are the example codes demonstrating the problems.

> devtools::install_github("kuppal2/xMWAS")
Downloading GitHub repo kuppal2/xMWAS@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: fields (14.0 -> 14.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 4
fields (14.0 -> 14.1) [CRAN]
Installing 1 packages: fields

  There is a binary version available but the source version is later:
       binary source needs_compilation
fields   14.0   14.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fields_14.0.tgz'
Content type 'application/x-gzip' length 4036552 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

The downloaded binary packages are in
    /var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T//RtmppYiBJK/downloaded_packages
✔  checking for file ‘/private/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T/RtmppYiBJK/remotes14bdb48f32e3f/kuppal2-xMWAS-a17fe32/DESCRIPTION’ ...
─  preparing ‘xMWAS’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘xMWAS_0.56.tar.gz’

* installing *source* package ‘xMWAS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GO.db’
Execution halted
ERROR: lazy loading failed for package ‘xMWAS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/xMWAS’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T//RtmppYiBJK/file14bdb67ab4d3f/xMWAS_0.56.tar.gz’ had non-zero exit status

> devtools::install_github("kuppal2/xMWAS")
Downloading GitHub repo kuppal2/xMWAS@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: fields (14.0 -> 14.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
✔  checking for file ‘/private/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T/RtmppYiBJK/remotes14bdb6e406073/kuppal2-xMWAS-a17fe32/DESCRIPTION’ ...
─  preparing ‘xMWAS’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘xMWAS_0.56.tar.gz’

* installing *source* package ‘xMWAS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GO.db’
Execution halted
ERROR: lazy loading failed for package ‘xMWAS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/xMWAS’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T//RtmppYiBJK/file14bdb447c5691/xMWAS_0.56.tar.gz’ had non-zero exit status

> devtools::install_github("kuppal2/xMWAS")
Downloading GitHub repo kuppal2/xMWAS@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: fields (14.0 -> 14.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
fields (14.0 -> 14.1) [CRAN]
Skipping 6 packages not available: AnnotationDbi, GO.db, preprocessCore, impute, RBGL, graph
Installing 5 packages: fields, AnnotationDbi, GO.db, preprocessCore, impute

  There is a binary version available but the source version is later:
       binary source needs_compilation
fields   14.0   14.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘fields’

trying URL 'https://cran.rstudio.com/src/contrib/fields_14.1.tar.gz'
Content type 'application/x-gzip' length 3483796 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

* installing *source* package ‘fields’ ...
** package ‘fields’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘fields’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/fields’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/fields’

The downloaded source packages are in
    ‘/private/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T/RtmppYiBJK/downloaded_packages’
✔  checking for file ‘/private/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T/RtmppYiBJK/remotes14bdb2f5354a0/kuppal2-xMWAS-a17fe32/DESCRIPTION’ ...
─  preparing ‘xMWAS’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘xMWAS_0.56.tar.gz’

* installing *source* package ‘xMWAS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GO.db’
Execution halted
ERROR: lazy loading failed for package ‘xMWAS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/xMWAS’
Warning messages:
1: packages ‘AnnotationDbi’, ‘GO.db’, ‘preprocessCore’, ‘impute’ are not available for this version of R

Versions of these packages 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 
2: In i.p(...) : installation of package ‘fields’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/var/folders/51/ty3l0kz95270xvvr237lmz9m0000gn/T//RtmppYiBJK/file14bdb567814ed/xMWAS_0.56.tar.gz’ had non-zero exit status