CRAN Package Check Results for Package BootstrapQTL

Last updated on 2021-01-24 07:50:42 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 2.59 40.77 43.36 OK
r-devel-linux-x86_64-debian-gcc 1.0.2 2.57 31.21 33.78 OK
r-devel-linux-x86_64-fedora-clang 1.0.2 62.71 OK
r-devel-linux-x86_64-fedora-gcc 1.0.2 54.77 OK
r-devel-windows-ix86+x86_64 1.0.2 7.00 65.00 72.00 NOTE
r-patched-linux-x86_64 1.0.2 3.00 39.14 42.14 OK
r-patched-solaris-x86 1.0.2 74.40 OK
r-release-linux-x86_64 1.0.2 3.35 39.10 42.45 OK
r-release-macos-x86_64 1.0.2 OK
r-release-windows-ix86+x86_64 1.0.2 6.00 63.00 69.00 ERROR
r-oldrel-macos-x86_64 1.0.2 NOTE
r-oldrel-windows-ix86+x86_64 1.0.2 5.00 50.00 55.00 ERROR

Check Details

Version: 1.0.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'doMC'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Check: tests
Result: ERROR
     Running 'testthat.R' [6s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(BootstrapQTL)
     Loading required package: MatrixEQTL
     >
     > test_check("BootstrapQTL")
     Registering 2 cores for bootstrap procedure.
     Mapping QTLs and obtaining nominal effect size estimates...
     Optimising data for bootstrap procedure...
     Running bootstrap procedure for 10 bootstraps on 2 cores.
     Removing winner's curse...
     Restoring global environment...
     Done!
     Restoring global environment...
     == Warnings ====================================================================
     -- Warning (test.R:47:3): Run BootstrapQTL -------------------------------------
     already exporting variable(s): cvrt, snps_boot, gene_boot, snpspos, genepos, bootstrap_file_directory, sig_pairs, tests_per_gene, local_correction, eSNP_threshold, errorCovariance, cisDist, useModel
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:47:2
     2. `%dopar%`(...)
     3. e$fun(obj, substitute(ex), parent.frame(), e$data)
     -- Warning (test.R:47:3): Run BootstrapQTL -------------------------------------
     3/10 bootstraps failed with error 'The number of covariates exceeds the number of samples.
     Linear regression can not be fit.' in the bootstrap estimation group.
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:47:2
     -- Warning (test.R:53:3): Run BootstrapQTL -------------------------------------
     cannot open file 'D:\temp\Rtmpmwl7oP\fileea3417682077': No such file or directory
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:53:2
     2. BootstrapQTL:::setupParallel(n_cores, verbose = TRUE, reporterCore = FALSE)
     3. parallel::makeCluster(nCores, type = "PSOCK")
     4. parallel::makePSOCKcluster(names = spec, ...)
     5. base::system(cmd, wait = FALSE, input = "")
     6. base::writeLines(input, f)
     7. base::file(con, "w")
    
     == Failed tests ================================================================
     -- Error (test.R:53:3): Run BootstrapQTL ---------------------------------------
     Error: cannot open the connection
     Backtrace:
     x
     1. \-BootstrapQTL::BootstrapQTL(...) test.R:53:2
     2. \-BootstrapQTL:::setupParallel(n_cores, verbose = TRUE, reporterCore = FALSE)
     3. \-parallel::makeCluster(nCores, type = "PSOCK")
     4. \-parallel::makePSOCKcluster(names = spec, ...)
     5. \-base::system(cmd, wait = FALSE, input = "")
     6. \-base::writeLines(input, f)
     7. \-base::file(con, "w")
    
     [ FAIL 1 | WARN 3 | SKIP 0 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.0.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘qvalue’
Flavor: r-oldrel-macos-x86_64

Version: 1.0.2
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘qvalue’
Flavor: r-oldrel-macos-x86_64

Version: 1.0.2
Check: tests
Result: ERROR
     Running 'testthat.R' [5s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(BootstrapQTL)
     Loading required package: MatrixEQTL
     >
     > test_check("BootstrapQTL")
     Registering 2 cores for bootstrap procedure.
     Mapping QTLs and obtaining nominal effect size estimates...
     Optimising data for bootstrap procedure...
     Running bootstrap procedure for 10 bootstraps on 2 cores.
     Removing winner's curse...
     Restoring global environment...
     Done!
     Restoring global environment...
     == Warnings ====================================================================
     -- Warning (test.R:47:3): Run BootstrapQTL -------------------------------------
     already exporting variable(s): cvrt, snps_boot, gene_boot, snpspos, genepos, bootstrap_file_directory, sig_pairs, tests_per_gene, local_correction, eSNP_threshold, errorCovariance, cisDist, useModel
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:47:2
     2. `%dopar%`(...)
     3. e$fun(obj, substitute(ex), parent.frame(), e$data)
     -- Warning (test.R:47:3): Run BootstrapQTL -------------------------------------
     1/10 bootstraps failed with error 'The number of covariates exceeds the number of samples.
     Linear regression can not be fit.' in the bootstrap estimation group.
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:47:2
     -- Warning (test.R:47:3): Run BootstrapQTL -------------------------------------
     1/10 bootstraps failed with error 'Colinear or zero covariates detected' in the bootstrap estimation group.
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:47:2
     -- Warning (test.R:53:3): Run BootstrapQTL -------------------------------------
     cannot open file 'D:\temp\RtmpMXBl2c\file1aab8601214b4': No such file or directory
     Backtrace:
     1. BootstrapQTL::BootstrapQTL(...) test.R:53:2
     2. BootstrapQTL:::setupParallel(n_cores, verbose = TRUE, reporterCore = FALSE)
     3. parallel::makeCluster(nCores, type = "PSOCK")
     4. parallel::makePSOCKcluster(names = spec, ...)
     5. parallel:::newPSOCKnode(names[[i]], options = options, rank = i)
     6. base::system(cmd, wait = FALSE, input = "")
     7. base::writeLines(input, f)
     8. base::file(con, "w")
    
     == Failed tests ================================================================
     -- Error (test.R:53:3): Run BootstrapQTL ---------------------------------------
     Error: cannot open the connection
     Backtrace:
     x
     1. \-BootstrapQTL::BootstrapQTL(...) test.R:53:2
     2. \-BootstrapQTL:::setupParallel(n_cores, verbose = TRUE, reporterCore = FALSE)
     3. \-parallel::makeCluster(nCores, type = "PSOCK")
     4. \-parallel::makePSOCKcluster(names = spec, ...)
     5. \-parallel:::newPSOCKnode(names[[i]], options = options, rank = i)
     6. \-base::system(cmd, wait = FALSE, input = "")
     7. \-base::writeLines(input, f)
     8. \-base::file(con, "w")
    
     [ FAIL 1 | WARN 4 | SKIP 0 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64