##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multiGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings multiGSEA_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'multiGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'multiGSEA' version '1.15.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'multiGSEA' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... WARNING
downloading 1 resources
retrieving 1 resource
loading from cache
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file '3c9857939b4_98538' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated 
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file '3c9857939b4_98538' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated 
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted

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
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file '3c9857939b4_98538' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated 
Execution halted
* checking dependencies in R code ... NOTE
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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
* checking S3 generic/method consistency ... WARNING
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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", 
           sQuo
Execution halted
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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", 
           sQuo
Execution halted
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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", 
           sQuo
Execution halted
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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", 
           sQuo
Execution halted
* checking Rd \usage sections ... NOTE
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'multiGSEA-Ex.R' failed
The error occurred in:


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "multiGSEA"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> base::assign(".ExTimings", "multiGSEA-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+   options(OutDec = '.')
+   format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
> 
> ### * </HEADER>
> library('multiGSEA')
loading from cache
Warning: file '3c9857939b4_98538' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(multiGSEA)
  loading from cache
  Error: package or namespace load failed for 'multiGSEA':
   .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
    call: NULL
    error: failed to load resource
    name: AH91792
    title: Mapping table of metabolite IDs and common names
    reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
  In addition: Warning message:
  file '3c9857939b4_98538' has magic number 'SQLit'
    Use of save versions prior to 2 is deprecated 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 8 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL multiGSEA
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'multiGSEA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
loading from cache
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
loading from cache
** testing if installed package can be loaded from final location
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (multiGSEA)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(multiGSEA)
loading from cache
Error: package or namespace load failed for 'multiGSEA':
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file '3c9857939b4_98538' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated 
Execution halted