Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:09:15 -0400 (Wed, 15 Apr 2020).
Package 568/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
FEM 3.14.0 Zhen Yang
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: FEM |
Version: 3.14.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FEM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FEM_3.14.0.tar.gz |
StartedAt: 2020-04-15 02:32:24 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 02:36:02 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 218.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: FEM.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FEM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FEM_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/FEM.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FEM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FEM’ version ‘3.14.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'AnnotationDbi', 'Matrix', 'marray', 'corrplot', 'igraph', 'impute', 'limma', 'org.Hs.eg.db', 'graph', 'BiocGenerics' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 for sufficient/correct file permissions ... OK * checking whether package ‘FEM’ can be installed ... WARNING Found the following significant warnings: Note: break used in wrong context: no loop is visible Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ See ‘/home/biocbuild/bbs-3.10-bioc/meat/FEM.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... NOTE installed size is 13.6Mb sub-directories of 1Mb or more: data 13.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘graph’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding * checking R 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 DoEpiMod: no visible global function definition for ‘mappedkeys’ DoEpiMod: no visible global function definition for ‘write.table’ DoExpMod: no visible global function definition for ‘mappedkeys’ DoExpMod: no visible global function definition for ‘write.table’ DoFEMbi: no visible global function definition for ‘mappedkeys’ DoFEMbi: no visible global function definition for ‘write.table’ FemModShow : mycircle : <anonymous>: no visible global function definition for ‘symbols’ FemModShow: no visible global function definition for ‘pdf’ FemModShow: no visible global function definition for ‘dev.off’ GenStatM: no visible global function definition for ‘data’ GenStatM: no visible binding for global variable ‘probe450kfemanno’ GenStatM: no visible binding for global variable ‘probeEPICfemanno’ GenStatM: no visible global function definition for ‘model.matrix’ GenStatMsp: no visible global function definition for ‘data’ GenStatMsp: no visible binding for global variable ‘probe450kfemanno’ GenStatMsp: no visible binding for global variable ‘probeEPICfemanno’ GenStatMsp: no visible global function definition for ‘model.matrix’ GenStatR: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: data dev.off mappedkeys model.matrix pdf probe450kfemanno probeEPICfemanno symbols write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "symbols") importFrom("stats", "model.matrix") importFrom("utils", "data", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: DoEpiMod.Rd:44-46: Dropping empty section \details prepare_Rd: DoEpiMod.Rd:71-73: Dropping empty section \note prepare_Rd: DoEpiMod.Rd:77-79: Dropping empty section \seealso prepare_Rd: DoExpMod.Rd:93: Dropping empty section \keyword prepare_Rd: DoExpMod.Rd:94: Dropping empty section \keyword prepare_Rd: DoExpMod.Rd:46-48: Dropping empty section \details prepare_Rd: DoExpMod.Rd:72-74: Dropping empty section \note prepare_Rd: DoExpMod.Rd:78-80: Dropping empty section \seealso prepare_Rd: DoFEMbi.Rd:45-47: Dropping empty section \details prepare_Rd: DoFEMbi.Rd:71-73: Dropping empty section \note prepare_Rd: DoFEMbi.Rd:77-79: Dropping empty section \seealso prepare_Rd: DoIntEpi450k.Rd:34-36: Dropping empty section \details prepare_Rd: DoIntEpi450k.Rd:52-54: Dropping empty section \note prepare_Rd: DoIntEpi450k.Rd:58-60: Dropping empty section \seealso prepare_Rd: DoIntEpi450k.Rd:61-63: Dropping empty section \examples prepare_Rd: DoIntExp.Rd:29-31: Dropping empty section \details prepare_Rd: DoIntExp.Rd:47-49: Dropping empty section \note prepare_Rd: DoIntExp.Rd:53-55: Dropping empty section \seealso prepare_Rd: DoIntExp.Rd:56-57: Dropping empty section \examples prepare_Rd: DoIntFEM450k.Rd:45-47: Dropping empty section \details prepare_Rd: DoIntFEM450k.Rd:64-66: Dropping empty section \note prepare_Rd: DoIntFEM450k.Rd:70-72: Dropping empty section \seealso prepare_Rd: DoIntFEM450k.Rd:73-75: Dropping empty section \examples prepare_Rd: FEM-package.Rd:47-48: Dropping empty section \seealso prepare_Rd: FEM-package.Rd:49-51: Dropping empty section \examples prepare_Rd: FemModShow.Rd:33-35: Dropping empty section \details prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \note prepare_Rd: FemModShow.Rd:53-55: Dropping empty section \seealso prepare_Rd: GenStatM.Rd:29-31: Dropping empty section \details prepare_Rd: GenStatM.Rd:47-49: Dropping empty section \note prepare_Rd: GenStatM.Rd:53-55: Dropping empty section \seealso prepare_Rd: GenStatM.Rd:56-58: Dropping empty section \examples prepare_Rd: GenStatMsp.Rd:32-34: Dropping empty section \details prepare_Rd: GenStatMsp.Rd:51-53: Dropping empty section \note prepare_Rd: GenStatMsp.Rd:57-59: Dropping empty section \seealso prepare_Rd: GenStatMsp.Rd:60-62: Dropping empty section \examples prepare_Rd: GenStatR.Rd:26-28: Dropping empty section \details prepare_Rd: GenStatR.Rd:43-45: Dropping empty section \note prepare_Rd: GenStatR.Rd:49-51: Dropping empty section \seealso prepare_Rd: GenStatR.Rd:52-54: Dropping empty section \examples prepare_Rd: Realdata.Rd:28-29: Dropping empty section \format prepare_Rd: Realdata.Rd:30-32: Dropping empty section \details prepare_Rd: Realdata.Rd:33-35: Dropping empty section \source prepare_Rd: Toydata.Rd:27-29: Dropping empty section \details prepare_Rd: Toydata.Rd:30-32: Dropping empty section \source prepare_Rd: probe450kfemanno.Rd:27-28: Dropping empty section \format prepare_Rd: probe450kfemanno.Rd:29-30: Dropping empty section \details prepare_Rd: probe450kfemanno.Rd:31-33: Dropping empty section \source prepare_Rd: probe450kfemanno.Rd:40-41: Dropping empty section \examples prepare_Rd: probeEPICfemanno.Rd:27-28: Dropping empty section \format prepare_Rd: probeEPICfemanno.Rd:29-30: Dropping empty section \details prepare_Rd: probeEPICfemanno.Rd:31-33: Dropping empty section \source prepare_Rd: probeEPICfemanno.Rd:40-41: Dropping empty section \examples * 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 ... WARNING Warning: package needs dependence on R (>= 2.10) * checking files in ‘vignettes’ ... NOTE The following files contain a license that requires distribution of original sources: ‘xcolor.sty’ Please ensure that you have complied with it. * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed FemModShow 12.288 0.844 13.310 DoFEMbi 7.632 0.020 7.758 DoEpiMod 7.568 0.004 8.698 DoExpMod 7.316 0.036 7.528 Toydata 7.040 0.064 7.249 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.10-bioc/meat/FEM.Rcheck/00check.log’ for details.
FEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL FEM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘FEM’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ ** testing if installed package keeps a record of temporary installation path * DONE (FEM)
FEM.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > BiocGenerics:::testPackage("FEM") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA corrplot 0.84 loaded Attaching package: 'igraph' The following object is masked from 'package:IRanges': union The following object is masked from 'package:S4Vectors': union The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'graph' The following objects are masked from 'package:igraph': degree, edges, intersection [1] ".setUp" [1] "Constructing weighted network" [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 [1] 11 [1] 12 [1] 13 [1] 14 [1] 15 [1] 16 [1] 17 [1] 18 [1] 19 [1] 20 [1] 21 [1] 22 [1] 23 [1] 24 [1] 25 [1] 26 [1] 27 [1] 28 [1] 29 [1] 30 [1] 31 [1] 32 [1] 33 [1] 34 [1] 35 [1] 36 [1] 37 [1] 38 [1] 39 [1] 40 [1] 41 [1] 42 [1] 43 [1] 44 [1] 45 [1] 46 [1] 47 [1] 48 [1] 49 [1] 50 [1] 51 [1] 52 [1] 53 [1] 54 [1] 55 [1] 56 [1] 57 [1] 58 [1] 59 [1] 60 [1] 61 [1] 62 [1] 63 [1] 64 [1] 65 [1] 66 [1] 67 [1] 68 [1] 69 [1] 70 [1] 71 [1] 72 [1] 73 [1] 74 [1] 75 [1] 76 [1] 77 [1] 78 [1] 79 [1] 80 [1] 81 [1] 82 [1] 83 [1] 84 [1] 85 [1] 86 [1] 87 [1] 88 [1] 89 [1] 90 [1] 91 [1] 92 [1] 93 [1] 94 [1] 95 [1] 96 [1] 97 [1] 98 [1] 99 [1] 100 [1] 101 [1] 102 [1] 103 [1] 104 [1] 105 [1] 106 [1] 107 [1] 108 [1] 109 [1] 110 [1] 111 [1] 112 [1] 113 [1] 114 [1] 115 [1] 116 [1] 117 [1] 118 [1] 119 [1] 120 [1] 121 [1] 122 [1] 123 [1] 124 [1] 125 [1] 126 [1] 127 [1] 128 [1] 129 [1] 130 [1] 131 [1] 132 [1] 133 [1] 134 [1] 135 [1] 136 [1] 137 [1] 138 [1] 139 [1] 140 [1] 141 [1] 142 [1] 143 [1] 144 [1] 145 [1] "Running Spin-Glass algorithm" [1] "Done for seed 1" [1] "Module Sizes=" 166929 36 [1] "Modularity values=" 166929 4.170086 [1] "Starting Monte Carlo Runs" [1] "Done for seed/module 1" 166929 0 [1] "Summarising and generating output" [1] 1 [1] "166929" RUNIT TEST PROTOCOL -- Wed Apr 15 02:35:59 2020 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : FEM RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 Warning messages: 1: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM' 2: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM' 3: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM' 4: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM' 5: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM' 6: replacing previous import 'igraph::path' by 'BiocGenerics::path' when loading 'FEM' 7: replacing previous import 'Matrix::which' by 'BiocGenerics::which' when loading 'FEM' 8: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM' 9: In write.table(out.m, file = paste("topFEMLists-", nameSTUDY, ".txt", : appending column names to file > > proc.time() user system elapsed 12.792 0.244 13.099
FEM.Rcheck/FEM-Ex.timings
name | user | system | elapsed | |
DoEpiMod | 7.568 | 0.004 | 8.698 | |
DoExpMod | 7.316 | 0.036 | 7.528 | |
DoFEMbi | 7.632 | 0.020 | 7.758 | |
FemModShow | 12.288 | 0.844 | 13.310 | |
Realdata | 0 | 0 | 0 | |
Toydata | 7.040 | 0.064 | 7.249 | |