Nothing
R/install.source.R
In groundhog: Version-Control for CRAN, GitHub, and GitLab Packages
Defines functions
install.source
install.source <- function(snowball,date,cores)
{
#Restart the feedback data.frame so that if they install something new it starts from scratch
on.exit(.pkgenv[['df.feedback']]<-NULL)
#0 Message if error
message_with_solutions <-
paste("Possible solutions:\n",
" 1) First, simply try again, the error may be a fluke.\n",
" 2) Inspect console log, you could be missing non-CRAN dependencies\n",
" (e.g., RTools for Windows, XQuartz for Mac, libssl for Ubuntu),\n",
" or have a connection problem, or another compatibility problem.\n",
" 3) If the error indicates that a dependency is missing, re-run the\n",
" groundhog.library() call with option `force.install=TRUE`\n",
" 4) If the package that failed is a dependency for a package you want,\n",
" you may install another version of that failed dependency directly\n",
" with a groundhog.library() call, just for that failing pkg, for a \n",
" different date. Then re-run this groundhog.library() call adding the\n",
" `ignore.deps` argument, to allowing the version mismatch for that pkg.\n",
" Use `toc(<pkg>)` to find out version release dates of 'pkg'.\n",
" 5) Similar to (4), use toc(<pkg>) to find the date for the next version\n",
" of the failing pkg and use a date after it for this entire\n",
" groundhog.library() call.\n",
" 6) Visit https://groundhogr.com/troubleshooting")
#1 Keep only source packages that are not yet installed
snowball <- snowball[snowball$from %in% c('source', 'github','gitlab') & snowball$installed==FALSE, ]
#1.5 early return if nothing to install
snowball$success = snowball$installed
if (nrow(snowball)==0) return(snowball)
#2 Get URL for installing each source
#2.1 Source files available as current pkgs (not in the archive)
ap_source <- get.current.packages("source")
#2.2 Basis of URL
repos <- as.character(getOption("repos"))
#2.3 Add url for source
snowball$source_url <- ifelse(snowball$pkg_vrs %in% ap_source$pkg_vrs,
paste0(repos , "/src/contrib/" ,snowball$pkg_vrs , ".tar.gz"),
paste0(repos , "/src/contrib/Archive/" ,snowball$pkg , "/" , snowball$pkg_vrs , ".tar.gz"))
#2.4 Modify default URL if a package is remote
#Check if snowball includes remote packages (it would have the column usr & sha)
if ("sha" %in% names(snowball))
{
#Find the remotes and instead of URL provide info remote::usr_pkg to install from clone
for (k in 1:nrow(snowball))
{
#If a sha is found, it's remote
if (!is.na(snowball$sha[k]))
{
#We figure out github vs gitlab from installation path
remote_id <- ''
if (regexpr('/_github/', snowball$installation.path[k])[[1]] > 0) remote_id <- 'github'
if (regexpr('/_gitlab/', snowball$installation.path[k])[[1]] > 0) remote_id <- 'gitlab'
#Then provide the 'url' (a ";;" separated string with all the fields needed to provide clone installation instructions)
snowball$source_url <- ifelse(!is.na(snowball$sha),
paste0("remote::",remote_id,"::",snowball$usr,"::",snowball$pkg,"::",date,"::",snowball$sha),
snowball$source_url)
#Note: this modified URL is then read by install.one.source (install.one.R) to install from clone
} #End if sha found
} #End loop remote
} #End if one remote at least
#2.5 Start message
message2("Will now install ",nrow(snowball), " packages from source")
if (cores>1 & nrow(snowball)>1)
{
#3.0 Message
message1("Will rely on `",cores, "` core processors for faster in-parallel installation")
message1("To force sequential installation set option `cores=1` in groundhog.library() ")
#3.1 Get snowflakes (snowball broken into parallel installable parts)
snowflakes <- get.snowflakes (snowball, date) #get.snowflakes.R
#3.2 Loop over snowflakes
for (k in 1:length(snowflakes))
{
#3.4 Get snowball subset for this snowflake
snowball.k <- snowball[snowball$pkg %in% snowflakes[[k]], ]
#3.5 Feedback
try(message.batch.installation.feedback(snowball,snowflakes,k,cores)) #message.batch.installation.feedback.R
#3.6 Subset the flake into 'source' vs remote
snowball.k_source <- snowball.k[snowball.k$from=='source',]
snowball.k_remote <- snowball.k[snowball.k$from!='source',]
n.source <-nrow(snowball.k_source)
n.remote <-nrow(snowball.k_remote)
#3.7 Install source in snowflake
if (n.source>0) {
utils::install.packages(snowball.k_source$source_url,repos=NULL, type='source', Ncpus=min(cores,n.source),
lib=snowball.k_source$installation.path)
}
#3.8 Install remotes in snowflake
if (n.remote>0) {
for (rk in 1:n.remote)
{
install.one (url=snowball.k_remote$source_url[rk])
}
}
#3.9 Check that everything was installed.
ip <- data.frame(utils::installed.packages(),stringsAsFactors = FALSE,row.names = NULL)
ip$pkg_vrs = paste0(ip$Package,"_",ip$Version)
snowflake.pkg_vrs <- snowball$pkg_vrs[snowball$pkg %in% snowflakes[[k]] ]
missing.pkg_vrs <- snowflake.pkg_vrs[!snowflake.pkg_vrs %in% ip$pkg_vrs]
#3.10 If it was not, error
if (length(missing.pkg_vrs)>0) {
message1("\nThe following package(s) from this batch failed to install:\n",pasteQC(missing.pkg_vrs))
message1("\n" , message_with_solutions)
message('\n\n -- Installation Failed -- ')
exit()
}
} #Loop installing snowflakes
} #End parallel installation
#4 Sequential installation
if (cores==1 | nrow(snowball)==1 )
{
#4.2 Start clock for install feedback k=1
start.time=Sys.time()
#4.3 Loop over individual packages
for (k in 1:length(snowball$source_url))
{
#Feedback
installation.feedback(k, date, snowball, start.time)
#Install
install.one (url=snowball$source_url[k])
#Verify installation
ip <- data.frame(utils::installed.packages(),stringsAsFactors = FALSE,row.names = NULL)
ip$pkg_vrs = paste0(ip$Package,"_",ip$Version)
if (!snowball$pkg_vrs[k] %in% ip$pkg_vrs) {
message1("\nThe package '",snowball$pkg_vrs[k],"' failed to install.")
message1("\n" , message_with_solutions)
message('\n\n -- Installation Failed -- ')
exit()
}
} #End install loop
} #End sequential install
}#End function install.source()
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groundhog documentation built on May 29, 2024, 7:55 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions install.source
install.source <- function(snowball,date,cores)
{
#Restart the feedback data.frame so that if they install something new it starts from scratch
on.exit(.pkgenv[['df.feedback']]<-NULL)
#0 Message if error
message_with_solutions <-
paste("Possible solutions:\n",
" 1) First, simply try again, the error may be a fluke.\n",
" 2) Inspect console log, you could be missing non-CRAN dependencies\n",
" (e.g., RTools for Windows, XQuartz for Mac, libssl for Ubuntu),\n",
" or have a connection problem, or another compatibility problem.\n",
" 3) If the error indicates that a dependency is missing, re-run the\n",
" groundhog.library() call with option `force.install=TRUE`\n",
" 4) If the package that failed is a dependency for a package you want,\n",
" you may install another version of that failed dependency directly\n",
" with a groundhog.library() call, just for that failing pkg, for a \n",
" different date. Then re-run this groundhog.library() call adding the\n",
" `ignore.deps` argument, to allowing the version mismatch for that pkg.\n",
" Use `toc(<pkg>)` to find out version release dates of 'pkg'.\n",
" 5) Similar to (4), use toc(<pkg>) to find the date for the next version\n",
" of the failing pkg and use a date after it for this entire\n",
" groundhog.library() call.\n",
" 6) Visit https://groundhogr.com/troubleshooting")
#1 Keep only source packages that are not yet installed
snowball <- snowball[snowball$from %in% c('source', 'github','gitlab') & snowball$installed==FALSE, ]
#1.5 early return if nothing to install
snowball$success = snowball$installed
if (nrow(snowball)==0) return(snowball)
#2 Get URL for installing each source
#2.1 Source files available as current pkgs (not in the archive)
ap_source <- get.current.packages("source")
#2.2 Basis of URL
repos <- as.character(getOption("repos"))
#2.3 Add url for source
snowball$source_url <- ifelse(snowball$pkg_vrs %in% ap_source$pkg_vrs,
paste0(repos , "/src/contrib/" ,snowball$pkg_vrs , ".tar.gz"),
paste0(repos , "/src/contrib/Archive/" ,snowball$pkg , "/" , snowball$pkg_vrs , ".tar.gz"))
#2.4 Modify default URL if a package is remote
#Check if snowball includes remote packages (it would have the column usr & sha)
if ("sha" %in% names(snowball))
{
#Find the remotes and instead of URL provide info remote::usr_pkg to install from clone
for (k in 1:nrow(snowball))
{
#If a sha is found, it's remote
if (!is.na(snowball$sha[k]))
{
#We figure out github vs gitlab from installation path
remote_id <- ''
if (regexpr('/_github/', snowball$installation.path[k])[[1]] > 0) remote_id <- 'github'
if (regexpr('/_gitlab/', snowball$installation.path[k])[[1]] > 0) remote_id <- 'gitlab'
#Then provide the 'url' (a ";;" separated string with all the fields needed to provide clone installation instructions)
snowball$source_url <- ifelse(!is.na(snowball$sha),
paste0("remote::",remote_id,"::",snowball$usr,"::",snowball$pkg,"::",date,"::",snowball$sha),
snowball$source_url)
#Note: this modified URL is then read by install.one.source (install.one.R) to install from clone
} #End if sha found
} #End loop remote
} #End if one remote at least
#2.5 Start message
message2("Will now install ",nrow(snowball), " packages from source")
if (cores>1 & nrow(snowball)>1)
{
#3.0 Message
message1("Will rely on `",cores, "` core processors for faster in-parallel installation")
message1("To force sequential installation set option `cores=1` in groundhog.library() ")
#3.1 Get snowflakes (snowball broken into parallel installable parts)
snowflakes <- get.snowflakes (snowball, date) #get.snowflakes.R
#3.2 Loop over snowflakes
for (k in 1:length(snowflakes))
{
#3.4 Get snowball subset for this snowflake
snowball.k <- snowball[snowball$pkg %in% snowflakes[[k]], ]
#3.5 Feedback
try(message.batch.installation.feedback(snowball,snowflakes,k,cores)) #message.batch.installation.feedback.R
#3.6 Subset the flake into 'source' vs remote
snowball.k_source <- snowball.k[snowball.k$from=='source',]
snowball.k_remote <- snowball.k[snowball.k$from!='source',]
n.source <-nrow(snowball.k_source)
n.remote <-nrow(snowball.k_remote)
#3.7 Install source in snowflake
if (n.source>0) {
utils::install.packages(snowball.k_source$source_url,repos=NULL, type='source', Ncpus=min(cores,n.source),
lib=snowball.k_source$installation.path)
}
#3.8 Install remotes in snowflake
if (n.remote>0) {
for (rk in 1:n.remote)
{
install.one (url=snowball.k_remote$source_url[rk])
}
}
#3.9 Check that everything was installed.
ip <- data.frame(utils::installed.packages(),stringsAsFactors = FALSE,row.names = NULL)
ip$pkg_vrs = paste0(ip$Package,"_",ip$Version)
snowflake.pkg_vrs <- snowball$pkg_vrs[snowball$pkg %in% snowflakes[[k]] ]
missing.pkg_vrs <- snowflake.pkg_vrs[!snowflake.pkg_vrs %in% ip$pkg_vrs]
#3.10 If it was not, error
if (length(missing.pkg_vrs)>0) {
message1("\nThe following package(s) from this batch failed to install:\n",pasteQC(missing.pkg_vrs))
message1("\n" , message_with_solutions)
message('\n\n -- Installation Failed -- ')
exit()
}
} #Loop installing snowflakes
} #End parallel installation
#4 Sequential installation
if (cores==1 | nrow(snowball)==1 )
{
#4.2 Start clock for install feedback k=1
start.time=Sys.time()
#4.3 Loop over individual packages
for (k in 1:length(snowball$source_url))
{
#Feedback
installation.feedback(k, date, snowball, start.time)
#Install
install.one (url=snowball$source_url[k])
#Verify installation
ip <- data.frame(utils::installed.packages(),stringsAsFactors = FALSE,row.names = NULL)
ip$pkg_vrs = paste0(ip$Package,"_",ip$Version)
if (!snowball$pkg_vrs[k] %in% ip$pkg_vrs) {
message1("\nThe package '",snowball$pkg_vrs[k],"' failed to install.")
message1("\n" , message_with_solutions)
message('\n\n -- Installation Failed -- ')
exit()
}
} #End install loop
} #End sequential install
}#End function install.source()
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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