Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1034/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
InterCellar 2.13.0 (landing page) Marta Interlandi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the InterCellar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterCellar.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: InterCellar |
Version: 2.13.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InterCellar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings InterCellar_2.13.0.tar.gz |
StartedAt: 2024-11-25 01:46:16 -0500 (Mon, 25 Nov 2024) |
EndedAt: 2024-11-25 01:49:40 -0500 (Mon, 25 Nov 2024) |
EllapsedTime: 204.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: InterCellar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InterCellar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings InterCellar_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 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 'InterCellar/DESCRIPTION' ... OK * this is package 'InterCellar' version '2.13.0' * 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 ... NOTE Found the following hidden files and directories: .dockerignore These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'InterCellar' 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 ... 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 buildPairsbyFunctionMatrix: warning in dcast(as.data.table(functions_df), int_pair ~ functional_term, fun = function(x) min(sum(x), 1), value.var = "value"): partial argument match of 'fun' to 'fun.aggregate' annotateGO: no visible binding for global variable 'go_linkage_type' annotateGO: no visible binding for global variable 'domain' annotateGO: no visible binding for global variable 'int_pair' annotateGO: no visible binding for global variable 'geneA' annotateGO: no visible binding for global variable 'geneB' annotateGO: no visible binding for global variable 'gene_symbol' annotateGO: no visible binding for global variable 'go_id' annotateGO: no visible binding for global variable 'geneA.1' annotateGO: no visible binding for global variable 'geneB.4' annotatePathways: no visible binding for global variable 'int_pair' annotatePathways: no visible binding for global variable 'geneA' annotatePathways: no visible binding for global variable 'geneB' combineAnnotations: no visible binding for global variable 'int_pair' combineAnnotations: no visible binding for global variable 'functional_term' createBarPlot1_ggplot: no visible binding for global variable 'cluster_names' createBarPlot1_ggplot: no visible binding for global variable 'n_int' createBarPlot1_ggplot: no visible binding for global variable 'type' createBarPlot2_ggplot: no visible binding for global variable 'Clusters' createBarPlot2_ggplot: no visible binding for global variable 'Num_int' getBack2BackBarplot: no visible binding for global variable 'n_int' getBack2BackBarplot: no visible binding for global variable 'cluster_names' getBack2BackBarplot: no visible binding for global variable 'type' getBack2BackBarplot: no visible binding for global variable 'diff_c1_c2' getBarplotDF : <anonymous>: no visible binding for global variable 'clustA' getBarplotDF : <anonymous>: no visible binding for global variable 'clustB' getBarplotDF : <anonymous>: no visible binding for global variable 'int.type' getBarplotDF : <anonymous>: no visible binding for global variable 'score' getBarplotDF2: no visible binding for global variable 'clustA' getBarplotDF2: no visible binding for global variable 'clustB' getClusterNetwork: no visible binding for global variable 'clustA' getClusterNetwork: no visible binding for global variable 'clustB' getClusterNetwork: no visible binding for global variable 'score' getClusterSize: no visible binding for global variable 'clustA' getClusterSize: no visible binding for global variable 'clustB' getDistinctCouplets: no visible binding for global variable 'clustA' getDistinctCouplets: no visible binding for global variable 'clustB' getDistinctCouplets: no visible binding for global variable 'int_pair' getDistinctCouplets: no visible binding for global variable 'cluster_pair' getDotPlot_selInt: no visible binding for global variable 'clustA' getDotPlot_selInt: no visible binding for global variable 'clustB' getDotPlot_selInt: no visible binding for global variable 'int_pair' getDotPlot_selInt: no visible binding for global variable 'cluster_pair' getDotPlot_selInt: no visible binding for global variable 'score' getGeneTable: no visible binding for global variable 'int_pair' getGeneTable: no visible binding for global variable 'geneA' getGeneTable: no visible binding for global variable 'geneB' getGeneTable: no visible binding for global variable 'typeA' getGeneTable: no visible binding for global variable 'typeB' getGeneTable: no visible binding for global variable 'annotation_strategy' getGeneTable: no visible binding for global variable 'pathway_cellchat' getGeneTable: no visible binding for global variable 'annotation_cellchat' getGeneTable: no visible binding for global variable 'evidence_cellchat' getGeneTable: no visible binding for global variable 'uniprotswissprot' getGeneTable: no visible binding for global variable 'ensembl_gene_id' getGeneTable: no visible binding for global variable 'hgnc_symbol' getIntFlow: no visible binding for global variable 'typeA' getIntFlow: no visible binding for global variable 'typeB' getIntFlow: no visible binding for global variable 'clustA' getIntFlow: no visible binding for global variable 'clustB' getPieChart: no visible binding for global variable 'condition' getPieChart: no visible binding for global variable 'value' getPieChart: no visible binding for global variable 'prop' getPieChart: no visible binding for global variable 'ypos' getPieChart: no visible binding for global variable 'perc' getRankedTerms: no visible binding for global variable 'functional_term' getRankedTerms: no visible binding for global variable 'int_pair' getRankedTerms: no visible binding for global variable 'n_occurrence' getSignif_table: no visible binding for global variable 'n_int_pair' getSignif_table: no visible binding for global variable 'n_cond' getSunburst: no visible binding for global variable 'clustA' getSunburst: no visible binding for global variable 'int_pair' getSunburst: no visible binding for global variable 'clustB' getSunburst: no visible binding for global variable 'score' getSunburst: no visible binding for global variable 'weightedInt' getUniqueDotplot: no visible binding for global variable 'int_pair' getUniqueDotplot: no visible binding for global variable 'cluster_pair' getUniqueDotplot: no visible binding for global variable 'condition' getUniqueIntpairs_byCond: no visible binding for global variable 'int_pair' getUniqueIntpairs_byCond: no visible binding for global variable 'condition' getUniqueIntpairs_byCond: no visible binding for global variable 'n_cond' getUniqueIntpairs_byCond: no visible binding for global variable 'clustA' getUniqueIntpairs_byCond: no visible binding for global variable 'clustB' getUniqueIntpairs_byCond: no visible binding for global variable 'clust_pair' mod_cluster_verse_server : <anonymous>: no visible binding for global variable 'clustA' mod_cluster_verse_server : <anonymous>: no visible binding for global variable 'clustB' mod_cluster_verse_server : <anonymous>: no visible binding for global variable 'score' mod_cluster_verse_server : <anonymous>: no visible binding for global variable 'int.type' mod_function_verse_server : <anonymous>: no visible binding for global variable 'GO_id' mod_function_verse_server : <anonymous>: no visible binding for global variable 'int_pair' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'scSignalR_specific' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'annotation_cellchat' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'pathway_cellchat' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'int_pair' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'clustA' mod_gene_verse_server : <anonymous>: no visible binding for global variable 'int.type' mod_int_pair_modules_server : <anonymous>: no visible binding for global variable 'int_pair' mod_int_pair_modules_server : <anonymous>: no visible binding for global variable 'int_pairModule' mod_int_pair_modules_server : <anonymous>: no visible binding for global variable 'p_value' mod_multi_cond_server : <anonymous>: no visible global function definition for 'legend' mod_multi_cond_server : <anonymous>: no visible binding for global variable 'clustA' mod_multi_cond_server : <anonymous>: no visible binding for global variable 'p_value' mod_multi_cond_server : <anonymous>: no visible binding for global variable 'condition' mod_multi_cond_server : <anonymous>: no visible binding for global variable 'int_pair' read.CPDBv2: no visible binding for global variable 'cluster_pair' read.CPDBv2: no visible binding for global variable 'mean_value' read.CPDBv2: no visible binding for global variable 'interacting_pair' read.CPDBv2: no visible binding for global variable 'p_value' read.icellnet: no visible binding for global variable 'X' read.icellnet: no visible binding for global variable 'score' updateInputLR: no visible binding for global variable 'typeA' updateInputLR: no visible binding for global variable 'typeB' updateInputLR: no visible binding for global variable 'int_pair' Undefined global functions or variables: Clusters GO_id Num_int X annotation_cellchat annotation_strategy clustA clustB clust_pair cluster_names cluster_pair condition diff_c1_c2 domain ensembl_gene_id evidence_cellchat functional_term geneA geneA.1 geneB geneB.4 gene_symbol go_id go_linkage_type hgnc_symbol int.type int_pair int_pairModule interacting_pair legend mean_value n_cond n_int n_int_pair n_occurrence p_value pathway_cellchat perc prop scSignalR_specific score type typeA typeB uniprotswissprot value weightedInt ypos Consider adding importFrom("graphics", "legend") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) getRadar_df.Rd:20-70: Lost braces 20 | cell_name){ | ^ checkRd: (-1) getRadar_df.Rd:21-24: Lost braces 21 | if(is.null(tab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:24-28: Lost braces 24 | } else { | ^ checkRd: (-1) getRadar_df.Rd:40-42: Lost braces 40 | if(is.null(lab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:42-44: Lost braces 42 | } else { | ^ checkRd: (-1) getRadar_df.Rd:107-157: Lost braces 107 | cell_name){ | ^ checkRd: (-1) getRadar_df.Rd:108-111: Lost braces 108 | if(is.null(tab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:111-115: Lost braces 111 | } else { | ^ checkRd: (-1) getRadar_df.Rd:127-129: Lost braces 127 | if(is.null(lab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:129-131: Lost braces 129 | } else { | ^ * 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 R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * 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: 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck/00check.log' for details.
InterCellar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL InterCellar ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'InterCellar' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (InterCellar)
InterCellar.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 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(InterCellar) > > test_check("InterCellar") [ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • interactive() is not TRUE (1): 'test-golem-recommended.R:24:5' [ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ] > > proc.time() user system elapsed 8.56 0.71 9.43
InterCellar.Rcheck/InterCellar-Ex.timings
name | user | system | elapsed | |
checkLL_RR | 0.07 | 0.23 | 0.31 | |
getClusterNames | 0.04 | 0.21 | 0.25 | |
getGeneTable | 0.28 | 0.22 | 0.50 | |
getIntFlow | 0.14 | 0.26 | 0.41 | |
run_app | 0 | 0 | 0 | |