Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:24 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SPONGE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPONGE.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1834/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SPONGE 1.14.0 (landing page) Markus List
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: SPONGE |
Version: 1.14.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SPONGE_1.14.0.tar.gz |
StartedAt: 2021-10-15 06:08:04 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 06:14:43 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 398.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SPONGE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SPONGE_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SPONGE.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.14.0' * 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 8.4Mb sub-directories of 1Mb or more: data 8.0Mb * 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 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 * 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 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 'is' 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 global function definition for 'is' 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 global function definition for 'is' 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 is k m mir mirna mscor mwhich p.adj p.val precomputed_cov_matrices solution sub.n Consider adding importFrom("methods", "is") importFrom("utils", "head") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 LazyData ... WARNING LazyData DB of 8.0 MB without LazyDataCompression set See ยง1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sponge_gene_miRNA_interaction_filter 23.61 0.10 23.70 sponge_build_null_model 13.67 0.02 13.69 sponge_run_benchmark 8.75 0.03 8.78 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sponge_gene_miRNA_interaction_filter 30.33 0.11 30.44 sponge_build_null_model 19.17 0.01 19.19 sponge_run_benchmark 11.50 0.03 11.54 * 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SPONGE.Rcheck/00check.log' for details.
SPONGE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SPONGE_1.14.0.tar.gz && rm -rf SPONGE.buildbin-libdir && mkdir SPONGE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPONGE.buildbin-libdir SPONGE_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SPONGE_1.14.0.zip && rm SPONGE_1.14.0.tar.gz SPONGE_1.14.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 5 4103k 5 221k 0 0 791k 0 0:00:05 --:--:-- 0:00:05 790k 66 4103k 66 2745k 0 0 2160k 0 0:00:01 0:00:01 --:--:-- 2160k 100 4103k 100 4103k 0 0 2155k 0 0:00:01 0:00:01 --:--:-- 2155k install for i386 Warning in untar2(tarfile, files, list, exdir, restore_times) : restoring symbolic link as a file copy * installing *source* package 'SPONGE' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 Warning in untar2(tarfile, files, list, exdir, restore_times) : restoring symbolic link as a file copy * installing *source* package 'SPONGE' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'SPONGE' as SPONGE_1.14.0.zip * DONE (SPONGE) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'SPONGE' successfully unpacked and MD5 sums checked
SPONGE.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ] > > proc.time() user system elapsed 72.78 0.93 87.42 |
SPONGE.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ] > > proc.time() user system elapsed 64.81 0.59 78.56 |
SPONGE.Rcheck/examples_i386/SPONGE-Ex.timings
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SPONGE.Rcheck/examples_x64/SPONGE-Ex.timings
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