CRAN Package Check Results for Package sglOptim

Last updated on 2017-02-24 23:52:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.5 44.64 162.97 207.61 NOTE
r-devel-linux-x86_64-debian-gcc 1.3.5 36.89 158.95 195.84 NOTE
r-devel-linux-x86_64-fedora-clang 1.3.5 345.58 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.3.5 341.23 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.3.5 254.68 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.3.5 151.00 498.00 649.00 OK
r-patched-linux-x86_64 1.3.5 33.68 168.75 202.43 OK
r-patched-solaris-sparc 1.3.5 2040.90 OK
r-patched-solaris-x86 1.3.5 192.60 ERROR
r-release-linux-x86_64 1.3.5 33.03 164.19 197.22 OK
r-release-osx-x86_64-mavericks 1.3.5 NOTE
r-release-windows-ix86+x86_64 1.3.5 120.00 474.00 594.00 OK
r-oldrel-windows-ix86+x86_64 1.3.5 135.00 654.00 789.00 OK

Check Details

Version: 1.3.5
Check: compiled code
Result: NOTE
    File ‘sglOptim/libs/sglOptim.so’:
     Found no call to: ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.3.5
Flags: --no-stop-on-test-error
Check: installed package size
Result: NOTE
     installed size is 7.9Mb
     sub-directories of 1Mb or more:
     libs 7.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.3.5
Flags: --no-stop-on-test-error
Check: foreign function calls
Result: NOTE
    Registration problems:
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim,
     args$groupWeights, args$parameterWeights, args$alpha, lambda,
     idx, algorithm.config)
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim,
     args$groupWeights, args$parameterWeights, args$alpha, d,
     lambda.min, lambda.min.rel, algorithm.config)
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, data, beta)
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data,
     args$block_dim, args$groupWeights, args$parameterWeights,
     args$alpha, lambda.list[[task]], algorithm.config)
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data,
     args$block_dim, args$groupWeights, args$parameterWeights,
     args$alpha, lambda.list[[task]], algorithm.config)
     symbol ‘call_sym’ in the local frame:
     .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim,
     args$groupWeights, args$parameterWeights, algorithm.config)
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.3.5
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘sglOptim/libs/sglOptim.so’:
     Found no call to: ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.3.5
Check: tests
Result: ERROR
     Running ‘A_lambda_run_tests.R’
     Running ‘B_fit_consistency_tests.R’
     Running ‘B_fit_run_tests_0.R’ [23s/24s]
    Running the tests in ‘tests/B_fit_run_tests_0.R’ failed.
    Complete output:
     > # SMALL CRAN TEST
     >
     > library(sglOptim)
     Loading required package: Matrix
     Loading required package: foreach
     Loading required package: doParallel
     Loading required package: iterators
     Loading required package: parallel
     > library(tools)
     >
     > source("units/run_tests.R")
     > source("units/generate_data.R")
     > source("units/fit_test.R")
     >
     > # warnings = errors
     > options(warn=2)
     > set.seed(100) # ensures consistency of tests
     >
     > # Run the tests
     >
     > ## create data
     > data <- create_test_data()
     >
     > ## Possible args values
     > values <- expand.grid(
     + grouping = list(
     + NULL,
     + factor(1:ncol(data$X) %% 3)
     + ),
     + groupWeights = list(NULL),
     + parameterWeights = list(NULL),
     + alpha = c(0, 0.5, 1),
     + d = 50,
     + lambda.min = 0.9,
     + lambda.min.rel = TRUE,
     + response = list(
     + NULL,
     + "link"
     + )
     + )
     >
     > ## consistency args values
     > consistency <- expand.grid(
     + sparseX = c(FALSE, TRUE),
     + sparseY = c(FALSE, TRUE),
     + objective = "linear_test_identity"
     + )
     >
     > run_tests(
     + data = data,
     + args_values = values,
     + args_consistency = consistency,
     + test = fit_test,
     + check_consistency = check_fit_consistency
     + )
     [1] "doing test 1 1"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     1 NULL NULL NULL 0 50 0.9 TRUE
     response
     1 NULL
     sparseX sparseY objective
     1 FALSE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 1 5
     10 0.98 1 5
     20 0.96 1 5
     30 0.94 2 10
     40 0.92 2 10
     50 0.90 2 10
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 19.1 19.059 19.018 ... 17.19
     [1] "doing test 1 2"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     1 NULL NULL NULL 0 50 0.9 TRUE
     response
     1 NULL
     sparseX sparseY objective
     2 TRUE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 1 5
     10 0.98 1 5
     20 0.96 1 5
     30 0.94 2 10
     40 0.92 2 10
     50 0.90 2 10
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 19.1 19.059 19.018 ... 17.19
     [1] "doing test 1 3"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     1 NULL NULL NULL 0 50 0.9 TRUE
     response
     1 NULL
     sparseX sparseY objective
     3 FALSE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 1 5
     10 0.98 1 5
     20 0.96 1 5
     30 0.94 2 10
     40 0.92 2 10
     50 0.90 2 10
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 19.1 19.059 19.018 ... 17.19
     [1] "doing test 1 4"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     1 NULL NULL NULL 0 50 0.9 TRUE
     response
     1 NULL
     sparseX sparseY objective
     4 TRUE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 1 5
     10 0.98 1 5
     20 0.96 1 5
     30 0.94 2 10
     40 0.92 2 10
     50 0.90 2 10
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 19.1 19.059 19.018 ... 17.19
     [1] "doing test 2 1"
     grouping groupWeights parameterWeights
     2 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1 NULL NULL
     alpha d lambda.min lambda.min.rel response
     2 0 50 0.9 TRUE NULL
     sparseX sparseY objective
     1 FALSE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 5 25
     20 0.96 5 25
     30 0.94 5 25
     40 0.92 5 25
     50 0.90 5 25
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 32.25 32.181 32.112 ... 29.025
     [1] "doing test 2 2"
     grouping groupWeights parameterWeights
     2 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1 NULL NULL
     alpha d lambda.min lambda.min.rel response
     2 0 50 0.9 TRUE NULL
     sparseX sparseY objective
     2 TRUE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 5 25
     20 0.96 5 25
     30 0.94 5 25
     40 0.92 5 25
     50 0.90 5 25
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 32.25 32.181 32.112 ... 29.025
     [1] "doing test 2 3"
     grouping groupWeights parameterWeights
     2 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1 NULL NULL
     alpha d lambda.min lambda.min.rel response
     2 0 50 0.9 TRUE NULL
     sparseX sparseY objective
     3 FALSE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 5 25
     20 0.96 5 25
     30 0.94 5 25
     40 0.92 5 25
     50 0.90 5 25
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 32.25 32.181 32.112 ... 29.025
     [1] "doing test 2 4"
     grouping groupWeights parameterWeights
     2 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1 NULL NULL
     alpha d lambda.min lambda.min.rel response
     2 0 50 0.9 TRUE NULL
     sparseX sparseY objective
     4 TRUE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 5 25
     20 0.96 5 25
     30 0.94 5 25
     40 0.92 5 25
     50 0.90 5 25
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 32.25 32.181 32.112 ... 29.025
     [1] "doing test 3 1"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     3 NULL NULL NULL 0.5 50 0.9 TRUE
     response
     3 NULL
     sparseX sparseY objective
     1 FALSE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 1 2
     20 0.96 1 2
     30 0.94 1 2
     40 0.92 1 2
     50 0.90 1 2
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 16.522 16.486 16.451 ... 14.87
     [1] "doing test 3 2"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     3 NULL NULL NULL 0.5 50 0.9 TRUE
     response
     3 NULL
     sparseX sparseY objective
     2 TRUE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 1 2
     20 0.96 1 2
     30 0.94 1 2
     40 0.92 1 2
     50 0.90 1 2
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 16.522 16.486 16.451 ... 14.87
     [1] "doing test 3 3"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     3 NULL NULL NULL 0.5 50 0.9 TRUE
     response
     3 NULL
     sparseX sparseY objective
     3 FALSE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 1 2
     20 0.96 1 2
     30 0.94 1 2
     40 0.92 1 2
     50 0.90 1 2
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 16.522 16.486 16.451 ... 14.87
     [1] "doing test 3 4"
     grouping groupWeights parameterWeights alpha d lambda.min lambda.min.rel
     3 NULL NULL NULL 0.5 50 0.9 TRUE
     response
     3 NULL
     sparseX sparseY objective
     4 TRUE TRUE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     Call:
     NULL
    
     Models:
    
     Index: Lambda: Features: Parameters:
     1 1.00 0 0
     10 0.98 1 2
     20 0.96 1 2
     30 0.94 1 2
     40 0.92 1 2
     50 0.90 1 2
    
    
     Call:
     NULL
    
     Predictions for 15 samples at 50 lambda values.
    
     Lambda values: 16.522 16.486 16.451 ... 14.87
     [1] "doing test 4 1"
     grouping groupWeights parameterWeights
     4 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1 NULL NULL
     alpha d lambda.min lambda.min.rel response
     4 0.5 50 0.9 TRUE NULL
     sparseX sparseY objective
     1 FALSE FALSE linear_test_identity
     0% 10 20 30 40 50 60 70 80 90 100%
     |----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Error in sgl_fit(module_name = module, PACKAGE = "sglOptim", data = data, :
     The algorithm has encountered a convergence problem
     Try/check the following:
     (1) Check the lambda sequence and try with a longer sequence (the length d should be larger than 100)
     (2) try with a larger lambda.min
     (3) Ensure minimum one sample from each group/class present in all subsample (or cross validation) sets used
     (Assert failed in ../inst/include/sgl/sgl_optimizer.h at line 234 )
     Calls: run_tests -> test -> sgl_fit -> .Call
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.3.5
Check: installed package size
Result: NOTE
     installed size is 9.0Mb
     sub-directories of 1Mb or more:
     libs 8.3Mb
Flavor: r-release-osx-x86_64-mavericks