Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:30:20 -0400 (Thu, 12 Apr 2018).
Package 1341/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SPONGE 1.0.3 Markus List
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: SPONGE |
Version: 1.0.3 |
Command: rm -rf SPONGE.buildbin-libdir SPONGE.Rcheck && mkdir SPONGE.buildbin-libdir SPONGE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SPONGE.buildbin-libdir SPONGE_1.0.3.tar.gz >SPONGE.Rcheck\00install.out 2>&1 && cp SPONGE.Rcheck\00install.out SPONGE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SPONGE.buildbin-libdir --install="check:SPONGE-install.out" --force-multiarch --no-vignettes --timings SPONGE_1.0.3.tar.gz |
StartedAt: 2018-04-12 03:23:28 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 03:31:33 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 485.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SPONGE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SPONGE.buildbin-libdir SPONGE.Rcheck && mkdir SPONGE.buildbin-libdir SPONGE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SPONGE.buildbin-libdir SPONGE_1.0.3.tar.gz >SPONGE.Rcheck\00install.out 2>&1 && cp SPONGE.Rcheck\00install.out SPONGE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SPONGE.buildbin-libdir --install="check:SPONGE-install.out" --force-multiarch --no-vignettes --timings SPONGE_1.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SPONGE.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SPONGE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SPONGE' version '1.0.3' * 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 'SPONGE' can be installed ... OK * checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: data 8.0Mb doc 1.5Mb * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkLambda: no visible binding for global variable 'i' check_and_convert_expression_data: no visible global function definition for 'attach.big.matrix' check_and_convert_expression_data: no visible global function definition for 'mwhich' compute_p_values: no visible binding for global variable 'cor_cut' compute_p_values: no visible binding for global variable 'df_cut' compute_p_values: no visible global function definition for 'J' compute_p_values: no visible binding for global variable '.I' compute_p_values: no visible binding for global variable '.EACHI' compute_p_values: no visible binding for global variable 'p.val' compute_p_values: no visible global function definition for ':=' compute_p_values: no visible binding for global variable 'p.adj' determine_cutoffs_for_null_model_partitioning: no visible global function definition for ':=' determine_cutoffs_for_null_model_partitioning: no visible binding for global variable 'cor_cut' determine_cutoffs_for_null_model_partitioning: no visible binding for global variable 'df_cut' fn_elasticnet: no visible binding for global variable 'alpha' fn_gene_miRNA_F_test: no visible binding for global variable 'mirna' fn_get_model_coef: no visible binding for global variable 'gene' isplitDT2 : nextEl: no visible global function definition for '.' processChunk: no visible binding for global variable 'geneA_idx' processChunk: no visible binding for global variable 'geneB_idx' processChunk: no visible binding for global variable 'geneA' processChunk: no visible binding for global variable 'geneB' processChunk: no visible binding for global variable 'mirna' sample_zero_mscor_cov: no visible binding for global variable 'solution' sample_zero_mscor_cov: no visible global function definition for 'ginv' sample_zero_mscor_cov: no visible binding for global variable 'i' sample_zero_mscor_data: no visible binding for global variable 'cov.matrix' sponge: no visible binding for global variable 'i' sponge: no visible global function definition for 'attach.big.matrix' sponge: no visible binding for global variable 'gene_combis' sponge_build_null_model: no visible binding for global variable 'precomputed_cov_matrices' sponge_build_null_model: no visible binding for global variable 'cov.matrices.m' sponge_build_null_model: no visible binding for global variable 'cov.matrices.k' sponge_build_null_model: no visible binding for global variable 'm' sponge_build_null_model: no visible binding for global variable 'k' sponge_compute_p_values: no visible binding for global variable 'dt.m' sponge_compute_p_values: no visible global function definition for ':=' sponge_compute_p_values: no visible binding for global variable 'cor_cut' sponge_compute_p_values: no visible binding for global variable 'df_cut' sponge_gene_miRNA_interaction_filter: no visible binding for global variable 'chunk' sponge_gene_miRNA_interaction_filter: no visible binding for global variable 'g_expr_batch' sponge_gene_miRNA_interaction_filter : <anonymous>: no visible binding for global variable 'g_expr_batch' sponge_gene_miRNA_interaction_filter: no visible binding for global variable 'gene' sponge_gene_miRNA_interaction_filter: no visible binding for global variable 'g_expr' sponge_network: no visible binding for global variable 'gene' sponge_network: no visible binding for global variable 'mir' sponge_plot_network_centralities: no visible global function definition for 'head' sponge_plot_simulation_results: no visible binding for global variable 'mscor' sponge_run_benchmark: no visible binding for global variable 'precomputed_cov_matrices' sponge_run_benchmark: no visible binding for global variable 'elastic.net' sponge_run_benchmark: no visible binding for global variable 'each.miRNA' sponge_subsampling: no visible binding for global variable 'sub.n' sponge_subsampling: no visible binding for global variable 'geneA' sponge_subsampling: no visible binding for global variable 'geneB' Undefined global functions or variables: . .EACHI .I := J alpha attach.big.matrix chunk cor_cut cov.matrices.k cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net g_expr g_expr_batch gene geneA geneA_idx geneB geneB_idx gene_combis ginv head i k m mir mirna mscor mwhich p.adj p.val precomputed_cov_matrices solution sub.n Consider adding importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed sponge_gene_miRNA_interaction_filter 26.64 0.12 26.77 sponge_build_null_model 12.92 0.00 12.92 sponge_run_benchmark 7.92 0.02 7.94 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed sponge_gene_miRNA_interaction_filter 36.78 0.06 36.85 sponge_build_null_model 20.77 0.03 20.80 sponge_run_benchmark 11.79 0.05 11.85 sponge_plot_simulation_results 5.46 0.03 5.48 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SPONGE.Rcheck/00check.log' for details.
SPONGE.Rcheck/00install.out
install for i386 * installing *source* package 'SPONGE' ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'SPONGE' finding HTML links ... done ceRNA_interactions html check_and_convert_expression_data html fn_elasticnet html fn_gene_miRNA_F_test html fn_get_model_coef html fn_get_rss html fn_get_shared_miRNAs html gene_expr html genes_pairwise_combinations html mir_expr html mir_interactions html mircode_ensg html mircode_symbol html precomputed_cov_matrices html precomputed_null_model html sample_zero_mscor_cov html sample_zero_mscor_data html sponge html sponge_build_null_model html sponge_compute_p_values html sponge_edge_centralities html sponge_gene_miRNA_interaction_filter html sponge_network html sponge_node_centralities html sponge_plot_network html sponge_plot_network_centralities html sponge_plot_simulation_results html sponge_run_benchmark html sponge_subsampling html targetscan_ensg html targetscan_symbol html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'SPONGE' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'SPONGE' as SPONGE_1.0.3.zip * DONE (SPONGE) In R CMD INSTALL In R CMD INSTALL
SPONGE.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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(SPONGE) > > test_check("SPONGE") == testthat results =========================================================== OK: 172 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 86.09 0.71 101.39 |
SPONGE.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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(SPONGE) > > test_check("SPONGE") == testthat results =========================================================== OK: 172 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 88.40 0.45 108.23 |
SPONGE.Rcheck/examples_i386/SPONGE-Ex.timings
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SPONGE.Rcheck/examples_x64/SPONGE-Ex.timings
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