Check results for 'ctsem'

using R Under development (unstable) (2025-06-27 r88363)
using platform: x86_64-pc-linux-gnu
R was compiled by clang version 20.1.7 flang version 20.1.7
running under: Fedora Linux 42 (Workstation Edition)
using session charset: UTF-8
using option ‘--no-stop-on-test-error’
checking for file ‘ctsem/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘ctsem’ version ‘3.10.3’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘ctsem’ can be installed ... [23m/30m] OK See the install log for details.
used C++ compiler: ‘clang version 20.1.7’
checking C++ specification ... OK
checking installed package size ... INFO installed size is 16.3Mb sub-directories of 1Mb or more: R 1.2Mb data 1.7Mb libs 12.0Mb
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [10s/15s] OK
checking whether the package can be loaded with stated dependencies ... [9s/12s] OK
checking whether the package can be unloaded cleanly ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: package or namespace load failed for ‘ctsem’: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
checking whether the namespace can be loaded with stated dependencies ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file.
checking whether the namespace can be unloaded cleanly ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
checking loading without being on the library search path ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Loading required package: Rcpp Error: package or namespace load failed for ‘ctsem’: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory It looks like this package has a loading problem when not on .libPaths: see the messages for details.
checking use of S3 registration ... OK
checking dependencies in R code ... NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
checking S3 generic/method consistency ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.
checking replacement functions ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory The argument of a replacement function which corresponds to the right hand side must be named ‘value’.
checking foreign function calls ... NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... ERROR Incorrect (un)loading of package shared object. shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory The system-specific extension for shared objects must not be added. See ?library.dynam. [28s/39s] NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Found the following possibly unsafe calls: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See section ‘Good practice’ in ‘?data’. shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 5: runHook(".onLoad", env, package.lib, package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
checking for missing documentation entries ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Error: package or namespace load failed for ‘ctsem’: .onLoad failed in loadNamespace() for 'parallelly', details: call: basename(pwd) error: a character vector argument expected Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.l Execution halted shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.