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quartet-rnaseq-report
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Fix dependencies.

tags/v0.1.1
YJC 3 年之前
父節點
557aeacf35
當前提交
d5bb973165
共有 5 個檔案被更改，包括 1219 行新增 和 84 行删除
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  1. +0
    -9
      resources/quartet_rnaseq_report.yaml
  2. +858
    -0
      resources/renv.lock
  3. +2
    -0
      resources/renv/.gitignore
  4. +359
    -55
      resources/renv/activate.R
  5. +0
    -20
      resources/renv/renv.lock

+ 0
- 9
resources/quartet_rnaseq_report.yaml 查看文件

@@ -1,9 +0,0 @@
run_modules:
- rnaseq_data_generation_information
- rnaseq_performance_assessment
- rnaseq_raw_qc
- rnaseq_post_alignment_qc
- rnaseq_quantification_qc
- rnaseq_supplementary

skip_generalstats: true

+ 858
- 0
resources/renv.lock 查看文件

@@ -0,0 +1,858 @@
{
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"Package": "spatial",
"Version": "7.3-11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f27a078d834614513608da2c08031130"
},
"stringi": {
"Package": "stringi",
"Version": "1.2.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bca4c3464ae356a8649d907944da78b4"
},
"stringr": {
"Package": "stringr",
"Version": "1.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0759e6b6c0957edb1311028a49a35e76"
},
"survival": {
"Package": "survival",
"Version": "3.1-8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ad25122f95d04988f6f79d69aaadd53d"
},
"sys": {
"Package": "sys",
"Version": "3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b227d13e29222b4574486cfcbde077fa"
},
"testthat": {
"Package": "testthat",
"Version": "2.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0829b987b8961fb07f3b1b64a2fbc495"
},
"tibble": {
"Package": "tibble",
"Version": "3.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08bd36bd34b20d4f7971d49e81deaab0"
},
"tidyr": {
"Package": "tidyr",
"Version": "0.8.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "95ded1450e6af17d0d3eb4b39233c43d"
},
"tidyselect": {
"Package": "tidyselect",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6ea435c354e8448819627cf686f66e0a"
},
"usethis": {
"Package": "usethis",
"Version": "1.6.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e1985f5a9985fea2e338fa7eb99018ca"
},
"utf8": {
"Package": "utf8",
"Version": "1.1.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4a5081acfb7b81a572e4384a7aaf2af1"
},
"vctrs": {
"Package": "vctrs",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5ba3006888ac62fd5e97b208d00d3317"
},
"viridisLite": {
"Package": "viridisLite",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ce4f6271baa94776db692f1cb2055bee"
},
"whisker": {
"Package": "whisker",
"Version": "0.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ca970b96d894e90397ed20637a0c1bbe"
},
"withr": {
"Package": "withr",
"Version": "2.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ecd17882a0b4419545691e095b74ee89"
},
"xfun": {
"Package": "xfun",
"Version": "0.16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b4106139b90981a8bfea9c10bab0baf1"
},
"xml2": {
"Package": "xml2",
"Version": "1.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2"
},
"xopen": {
"Package": "xopen",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6c85f015dee9cc7710ddd20f86881f58"
},
"yaml": {
"Package": "yaml",
"Version": "2.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2826c5d9efb0a88f657c7a679c7106db"
}
}
}

+ 2
- 0
resources/renv/.gitignore 查看文件

@@ -1,3 +1,5 @@
library/
local/
lock/
python/
staging/

+ 359
- 55
resources/renv/activate.R 查看文件

@@ -2,7 +2,7 @@
local({

# the requested version of renv
version <- "0.12.0"
version <- "0.13.0"

# the project directory
project <- getwd()
@@ -39,16 +39,6 @@ local({
# load bootstrap tools
bootstrap <- function(version, library) {
# read repos (respecting override if set)
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
if (is.na(repos))
repos <- getOption("repos")
# fix up repos
on.exit(options(repos = repos), add = TRUE)
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
options(repos = repos)
# attempt to download renv
tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
if (inherits(tarball, "error"))
@@ -61,6 +51,66 @@ local({
}
renv_bootstrap_tests_running <- function() {
getOption("renv.tests.running", default = FALSE)
}
renv_bootstrap_repos <- function() {
# check for repos override
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
if (!is.na(repos))
return(repos)
# if we're testing, re-use the test repositories
if (renv_bootstrap_tests_running())
return(getOption("renv.tests.repos"))
# retrieve current repos
repos <- getOption("repos")
# ensure @CRAN@ entries are resolved
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
# add in renv.bootstrap.repos if set
default <- c(FALLBACK = "https://cloud.r-project.org")
extra <- getOption("renv.bootstrap.repos", default = default)
repos <- c(repos, extra)
# remove duplicates that might've snuck in
dupes <- duplicated(repos) | duplicated(names(repos))
repos[!dupes]
}
renv_bootstrap_download <- function(version) {
# if the renv version number has 4 components, assume it must
# be retrieved via github
nv <- numeric_version(version)
components <- unclass(nv)[[1]]
methods <- if (length(components) == 4L) {
list(
renv_bootstrap_download_github
)
} else {
list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive
)
}
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
stop("failed to download renv ", version)
}
renv_bootstrap_download_impl <- function(url, destfile) {
mode <- "wb"
@@ -73,7 +123,7 @@ local({
if (fixup)
mode <- "w+b"
download.file(
utils::download.file(
url = url,
destfile = destfile,
mode = mode,
@@ -82,60 +132,92 @@ local({
}
renv_bootstrap_download <- function(version) {
methods <- list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive,
renv_bootstrap_download_github
)
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
renv_bootstrap_download_cran_latest <- function(version) {
stop("failed to download renv ", version)
repos <- renv_bootstrap_download_cran_latest_find(version)
}
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
renv_bootstrap_download_cran_latest <- function(version) {
downloader <- function(type) {
# check for renv on CRAN matching this version
db <- as.data.frame(available.packages(), stringsAsFactors = FALSE)
tryCatch(
utils::download.packages(
pkgs = "renv",
destdir = tempdir(),
repos = repos,
type = type,
quiet = TRUE
),
condition = identity
)
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
if (nrow(entry) == 0) {
fmt <- "renv %s is not available from your declared package repositories"
stop(sprintf(fmt, version))
}
message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
info <- tryCatch(
download.packages("renv", destdir = tempdir()),
condition = identity
)
# first, try downloading a binary on Windows + macOS if appropriate
binary <-
!identical(.Platform$pkgType, "source") &&
!identical(getOption("pkgType"), "source") &&
Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
if (binary) {
info <- downloader(type = "binary")
if (!inherits(info, "condition")) {
message("OK (downloaded binary)")
return(info[1, 2])
}
}
# otherwise, try downloading a source tarball
info <- downloader(type = "source")
if (inherits(info, "condition")) {
message("FAILED")
return(FALSE)
}
message("OK")
# report success and return
message("OK (downloaded source)")
info[1, 2]
}
renv_bootstrap_download_cran_latest_find <- function(version) {
all <- renv_bootstrap_repos()
for (repos in all) {
db <- tryCatch(
as.data.frame(
x = utils::available.packages(repos = repos),
stringsAsFactors = FALSE
),
error = identity
)
if (inherits(db, "error"))
next
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
if (nrow(entry) == 0)
next
return(repos)
}
fmt <- "renv %s is not available from your declared package repositories"
stop(sprintf(fmt, version))
}
renv_bootstrap_download_cran_archive <- function(version) {
name <- sprintf("renv_%s.tar.gz", version)
repos <- getOption("repos")
repos <- renv_bootstrap_repos()
urls <- file.path(repos, "src/contrib/Archive/renv", name)
destfile <- file.path(tempdir(), name)
message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
for (url in urls) {
@@ -194,7 +276,7 @@ local({
return(FALSE)
}
message("Done!")
message("OK")
return(destfile)
}
@@ -226,7 +308,7 @@ local({
}
renv_bootstrap_prefix <- function() {
renv_bootstrap_platform_prefix <- function() {
# construct version prefix
version <- paste(R.version$major, R.version$minor, sep = ".")
@@ -245,8 +327,8 @@ local({
components <- c(prefix, R.version$platform)
# include prefix if provided by user
prefix <- Sys.getenv("RENV_PATHS_PREFIX")
if (nzchar(prefix))
prefix <- renv_bootstrap_platform_prefix_impl()
if (!is.na(prefix) && nzchar(prefix))
components <- c(prefix, components)
# build prefix
@@ -254,6 +336,152 @@ local({
}
renv_bootstrap_platform_prefix_impl <- function() {
# if an explicit prefix has been supplied, use it
prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
if (!is.na(prefix))
return(prefix)
# if the user has requested an automatic prefix, generate it
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
if (auto %in% c("TRUE", "True", "true", "1"))
return(renv_bootstrap_platform_prefix_auto())
# empty string on failure
""
}
renv_bootstrap_platform_prefix_auto <- function() {
prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
if (inherits(prefix, "error") || prefix %in% "unknown") {
msg <- paste(
"failed to infer current operating system",
"please file a bug report at https://github.com/rstudio/renv/issues",
sep = "; "
)
warning(msg)
}
prefix
}
renv_bootstrap_platform_os <- function() {
sysinfo <- Sys.info()
sysname <- sysinfo[["sysname"]]
# handle Windows + macOS up front
if (sysname == "Windows")
return("windows")
else if (sysname == "Darwin")
return("macos")
# check for os-release files
for (file in c("/etc/os-release", "/usr/lib/os-release"))
if (file.exists(file))
return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
# check for redhat-release files
if (file.exists("/etc/redhat-release"))
return(renv_bootstrap_platform_os_via_redhat_release())
"unknown"
}
renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
# read /etc/os-release
release <- utils::read.table(
file = file,
sep = "=",
quote = c("\"", "'"),
col.names = c("Key", "Value"),
comment.char = "#",
stringsAsFactors = FALSE
)
vars <- as.list(release$Value)
names(vars) <- release$Key
# get os name
os <- tolower(sysinfo[["sysname"]])
# read id
id <- "unknown"
for (field in c("ID", "ID_LIKE")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
id <- vars[[field]]
break
}
}
# read version
version <- "unknown"
for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
version <- vars[[field]]
break
}
}
# join together
paste(c(os, id, version), collapse = "-")
}
renv_bootstrap_platform_os_via_redhat_release <- function() {
# read /etc/redhat-release
contents <- readLines("/etc/redhat-release", warn = FALSE)
# infer id
id <- if (grepl("centos", contents, ignore.case = TRUE))
"centos"
else if (grepl("redhat", contents, ignore.case = TRUE))
"redhat"
else
"unknown"
# try to find a version component (very hacky)
version <- "unknown"
parts <- strsplit(contents, "[[:space:]]")[[1L]]
for (part in parts) {
nv <- tryCatch(numeric_version(part), error = identity)
if (inherits(nv, "error"))
next
version <- nv[1, 1]
break
}
paste(c("linux", id, version), collapse = "-")
}
renv_bootstrap_library_root_name <- function(project) {
# use project name as-is if requested
asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
if (asis)
return(basename(project))
# otherwise, disambiguate based on project's path
id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
paste(basename(project), id, sep = "-")
}
renv_bootstrap_library_root <- function(project) {
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
@@ -261,10 +489,13 @@ local({
return(path)
path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
if (!is.na(path))
return(file.path(path, basename(project)))
if (!is.na(path)) {
name <- renv_bootstrap_library_root_name(project)
return(file.path(path, name))
}
file.path(project, "renv/library")
prefix <- renv_bootstrap_profile_prefix()
paste(c(project, prefix, "renv/library"), collapse = "/")
}
@@ -283,8 +514,8 @@ local({
paste("renv", loadedversion, sep = "@")
fmt <- paste(
"renv %1$s was loaded from project library, but renv %2$s is recorded in lockfile.",
"Use `renv::record(\"%3$s\")` to record this version in the lockfile.",
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
"Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
sep = "\n"
)
@@ -296,6 +527,16 @@ local({
}
renv_bootstrap_hash_text <- function(text) {
hashfile <- tempfile("renv-hash-")
on.exit(unlink(hashfile), add = TRUE)
writeLines(text, con = hashfile)
tools::md5sum(hashfile)
}
renv_bootstrap_load <- function(project, libpath, version) {
# try to load renv from the project library
@@ -311,12 +552,69 @@ local({
TRUE
}
renv_bootstrap_profile_load <- function(project) {
# if RENV_PROFILE is already set, just use that
profile <- Sys.getenv("RENV_PROFILE", unset = NA)
if (!is.na(profile) && nzchar(profile))
return(profile)
# check for a profile file (nothing to do if it doesn't exist)
path <- file.path(project, "renv/local/profile")
if (!file.exists(path))
return(NULL)
# read the profile, and set it if it exists
contents <- readLines(path, warn = FALSE)
if (length(contents) == 0L)
return(NULL)
# set RENV_PROFILE
profile <- contents[[1L]]
if (nzchar(profile))
Sys.setenv(RENV_PROFILE = profile)
profile
}
renv_bootstrap_profile_prefix <- function() {
profile <- renv_bootstrap_profile_get()
if (!is.null(profile))
return(file.path("renv/profiles", profile))
}
renv_bootstrap_profile_get <- function() {
profile <- Sys.getenv("RENV_PROFILE", unset = "")
renv_bootstrap_profile_normalize(profile)
}
renv_bootstrap_profile_set <- function(profile) {
profile <- renv_bootstrap_profile_normalize(profile)
if (is.null(profile))
Sys.unsetenv("RENV_PROFILE")
else
Sys.setenv(RENV_PROFILE = profile)
}
renv_bootstrap_profile_normalize <- function(profile) {
if (is.null(profile) || profile %in% c("", "default"))
return(NULL)
profile
}

# load the renv profile, if any
renv_bootstrap_profile_load(project)

# construct path to library root
root <- renv_bootstrap_library_root(project)

# construct library prefix for platform
prefix <- renv_bootstrap_prefix()
prefix <- renv_bootstrap_platform_prefix()

# construct full libpath
libpath <- file.path(root, prefix)
@@ -325,7 +623,13 @@ local({
if (renv_bootstrap_load(project, libpath, version))
return(TRUE)

# load failed; attempt to bootstrap
# load failed; inform user we're about to bootstrap
prefix <- paste("# Bootstrapping renv", version)
postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
header <- paste(prefix, postfix)
message(header)

# perform bootstrap
bootstrap(version, libpath)

# exit early if we're just testing bootstrap
@@ -334,7 +638,7 @@ local({

# try again to load
if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
message("Successfully installed and loaded renv ", version, ".")
message("* Successfully installed and loaded renv ", version, ".")
return(renv::load())
}


+ 0
- 20
resources/renv/renv.lock 查看文件

@@ -1,20 +0,0 @@
{
"R": {
"Version": "3.6.3",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"Packages": {
"renv": {
"Package": "renv",
"Version": "0.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9f10d9db5b50400c348920c5c603385e"
}
}
}

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