Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-09-11 10:30:55 -0400 (Tue, 11 Sep 2018).
Package 1128/1560 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ProCoNA 1.18.0 David L Gibbs
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: ProCoNA |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ProCoNA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ProCoNA_1.18.0.tar.gz |
StartedAt: 2018-09-11 02:55:42 -0400 (Tue, 11 Sep 2018) |
EndedAt: 2018-09-11 02:58:57 -0400 (Tue, 11 Sep 2018) |
EllapsedTime: 195.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ProCoNA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ProCoNA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ProCoNA_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ProCoNA.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ProCoNA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ProCoNA’ version ‘1.18.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ProCoNA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Malformed Description field: should contain one or more complete sentences. * 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 * 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 bootstrapProconaNetwork: no visible global function definition for ‘as.dist’ bootstrapProconaNetwork: no visible global function definition for ‘cutreeDynamic’ buildProconaNetwork: no visible global function definition for ‘as.dist’ buildProconaNetwork: no visible global function definition for ‘cutreeDynamic’ MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global function definition for ‘pdf’ MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global function definition for ‘dev.off’ correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric: no visible global function definition for ‘par’ correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric: no visible global function definition for ‘pdf’ correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric: no visible global function definition for ‘dev.off’ getFisherMatrix,character-character-numeric-numeric: no visible global function definition for ‘fisher.test’ peptideConnectivityTest,proconaNet-data.frame-character-character-numeric: no visible global function definition for ‘t.test’ peptideCorrelationTest,matrix-data.frame-character-character: no visible global function definition for ‘t.test’ Undefined global functions or variables: as.dist cutreeDynamic dev.off fisher.test par pdf t.test Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "par") importFrom("stats", "as.dist", "fisher.test", "t.test") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed bootstrapProconaNetwork 6.548 0.032 6.586 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/ProCoNA.Rcheck/00check.log’ for details.
ProCoNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ProCoNA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘ProCoNA’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=20 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=20 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded ========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=20 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=20 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== * DONE (ProCoNA)
ProCoNA.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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. > require("ProCoNA") || stop("unable to load MyPackage") Loading required package: ProCoNA Loading required package: WGCNA Loading required package: dynamicTreeCut Loading required package: fastcluster Attaching package: 'fastcluster' The following object is masked from 'package:stats': hclust ========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=20 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=20 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Attaching package: 'WGCNA' The following object is masked from 'package:stats': cor Loading required package: MSnbase Loading required package: BiocGenerics Loading required package: parallel 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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: BiocParallel Loading required package: ProtGenerics This is MSnbase version 2.6.3 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:stats': smooth The following object is masked from 'package:base': trimws Loading required package: flashClust Attaching package: 'flashClust' The following object is masked from 'package:fastcluster': hclust The following object is masked from 'package:stats': hclust Attaching package: 'ProCoNA' The following object is masked from 'package:ProtGenerics': peptides The following object is masked from 'package:Biobase': samples [1] TRUE > BiocGenerics:::testPackage("ProCoNA") Constructing New ProCoNA Network Object Using power: 1 Computing adjacency Computing TOM ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. Clustering ..cutHeight not given, setting it to 0.461 ===> 99% of the (truncated) height range in dendro. ..done. 0 1 2 3 4 4 174 127 92 77 Merging modules mergeCloseModules: Merging modules whose distance is less than 0.1 .. will look for grey label ME0 multiSetMEs: Calculating module MEs. Working on set 1 ... moduleEigengenes : Working on ME for module 1 moduleEigengenes : Working on ME for module 2 moduleEigengenes : Working on ME for module 3 moduleEigengenes : Working on ME for module 4 Changing original colors: 1 to 1 2 to 2 3 to 3 4 to 4 Calculating new MEs... multiSetMEs: Calculating module MEs. Working on set 1 ... moduleEigengenes : Working on ME for module 0 moduleEigengenes : Working on ME for module 1 moduleEigengenes : Working on ME for module 2 moduleEigengenes : Working on ME for module 3 moduleEigengenes : Working on ME for module 4 Topological Overlap Permutation Test On Modules Permuting module: 1 dim of TOM: 174174 Permuting module: 2 dim of TOM: 127127 Permuting module: 3 dim of TOM: 9292 Permuting module: 4 dim of TOM: 7777 DONE! [1] "module analysis: 1" [1] "probes that pass Kme and are within module: 122" [1] "of these, 26 are relevant to our PI network..." [1] "found 4 in the first column" [1] "found 3 in the second column" [1] "1 observed edges" [1] "pvalue: 0.033" [1] "*****" [1] "module analysis: 2" [1] "probes that pass Kme and are within module: 123" [1] "of these, 65 are relevant to our PI network..." [1] "found 6 in the first column" [1] "found 8 in the second column" [1] "6 observed edges" [1] "pvalue: 0" [1] "*****" [1] "module analysis: 3" [1] "probes that pass Kme and are within module: 92" [1] "of these, 0 are relevant to our PI network..." [1] "ERROR: no probes meet Kme threshold within module" [1] "module analysis: 0" [1] "probes that pass Kme and are within module: 4" [1] "of these, 0 are relevant to our PI network..." [1] "ERROR: no probes meet Kme threshold within module" [1] "module analysis: 4" [1] "probes that pass Kme and are within module: 74" [1] "of these, 8 are relevant to our PI network..." [1] "found 2 in the first column" [1] "found 1 in the second column" [1] "1 observed edges" [1] "pvalue: 0.007" [1] "*****" Permuting module: 1 dim of TOM: 100100 Permuting module: 2 dim of TOM: 100100 Permuting module: 3 dim of TOM: 100100 Permuting module: 4 dim of TOM: 100100 Permuting module: 5 dim of TOM: 100100 RUNIT TEST PROTOCOL -- Tue Sep 11 02:58:55 2018 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : ProCoNA RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 11.404 0.348 12.325
ProCoNA.Rcheck/ProCoNA-Ex.timings
name | user | system | elapsed | |
MMvsPS | 0.232 | 0.004 | 0.263 | |
MMvsPSallModules | 0 | 0 | 0 | |
accessors | 0.668 | 0.000 | 0.670 | |
bootstrapProconaNetwork | 6.548 | 0.032 | 6.586 | |
buildProconaNetwork | 2.596 | 0.004 | 2.605 | |
compareNetworksWithFishersExactTest | 0.004 | 0.000 | 0.001 | |
compareNetworksWithFishersExactTestProcona | 0 | 0 | 0 | |
corBootstrap | 1.456 | 0.012 | 1.469 | |
correlationWithPhenotypesHeatMap | 4.784 | 0.092 | 4.878 | |
getFisherMatrix | 0.296 | 0.008 | 0.303 | |
goStatTest | 0.004 | 0.000 | 0.000 | |
hclust | 0.000 | 0.000 | 0.001 | |
moduleMemberCorrelations | 0.344 | 0.004 | 0.346 | |
modulePhenotypeCorrelations | 0.200 | 0.000 | 0.199 | |
peptideConnectivityTest | 1.268 | 0.012 | 1.280 | |
peptideCorrelationTest | 2.748 | 0.004 | 2.751 | |
plotNet | 0.208 | 0.000 | 0.209 | |
ppiPermTest | 0.272 | 0.000 | 0.270 | |
printNet | 0.000 | 0.000 | 0.001 | |
subsetPeptideData | 0.276 | 0.048 | 0.322 | |
toPermTest | 0.284 | 0.000 | 0.283 | |
utri | 0.000 | 0.000 | 0.001 | |