Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:03 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the geneXtendeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/geneXtendeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 740/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geneXtendeR 1.20.0 (landing page) Bohdan Khomtchouk
| nebbiolo2 | Linux (Ubuntu 20.04.4 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 | ERROR | OK | |||||||||
Package: geneXtendeR |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneXtendeR_1.20.0.tar.gz |
StartedAt: 2022-04-12 13:37:51 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 13:56:56 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 1144.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: geneXtendeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneXtendeR_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/geneXtendeR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.20.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘geneXtendeR’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.7Mb sub-directories of 1Mb or more: data 6.1Mb doc 1.9Mb extdata 3.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rtracklayer’ 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 ... 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 ... NOTE Namespaces in Imports field not imported from: ‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .geneXtender: no visible binding for global variable ‘type’ .geneXtender: no visible binding for global variable ‘seqid’ .geneXtender: no visible binding for global variable ‘gene_id’ .geneXtender: no visible binding for global variable ‘gene_name’ annotate_n: no visible binding for global variable ‘..I’ annotate_n: no visible binding for global variable ‘seqid’ diffGO: no visible binding for global variable ‘rat’ gene_annotate: no visible global function definition for ‘.’ gene_annotate: no visible binding for global variable ‘Distance-of-Gene-to-Nearest-Peak’ gene_annotate: no visible global function definition for ‘sd’ gene_annotate: no visible binding for global variable ‘Chromosome’ gene_annotate: no visible binding for global variable ‘Gene-Start’ gene_annotate: no visible binding for global variable ‘Gene-End’ gene_annotate: no visible binding for global variable ‘Gene-ID’ gene_annotate: no visible binding for global variable ‘Gene-Name’ gene_annotate: no visible binding for global variable ‘Peaks-on-Gene-Body’ gene_annotate: no visible binding for global variable ‘Number-of-Peaks-Associated-with-Gene’ gene_lookup: no visible binding for global variable ‘gene_name_id’ gene_lookup: no visible binding for global variable ‘gene_id’ gene_lookup : internal_find: no visible binding for global variable ‘Chromosome’ gene_lookup : internal_find: no visible binding for global variable ‘distance’ gene_lookup : internal_find: no visible global function definition for ‘na.omit’ gene_lookup: no visible binding for global variable ‘..I’ gene_lookup: no visible binding for global variable ‘distance’ makeWordCloud: no visible binding for global variable ‘rat’ meanPeakLength: no visible binding for global variable ‘rat’ peaksInput: no visible binding for global variable ‘chr’ peaksInput: no visible global function definition for ‘na.omit’ peaksMerge: no visible binding for global variable ‘chr’ peaksMerge: no visible binding for global variable ‘g’ peaksMerge: no visible global function definition for ‘.’ plotWordFreq : geneXtender: no visible binding for global variable ‘type’ plotWordFreq : geneXtender: no visible binding for global variable ‘seqid’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_id’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_name’ Undefined global functions or variables: . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id na.omit rat sd seqid type Consider adding importFrom("stats", "na.omit", "sd") 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 LazyData ... WARNING LazyData DB of 5.8 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE Files named as vignettes but with no recognized vignette engine: ‘vignettes/geneXtendeR.Rnw’ (Is a VignetteBuilder field missing?) * checking examples ... ERROR Running examples in ‘geneXtendeR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: hotspotPlot > ### Title: Graphs hotspots of statistically significant peak activity. > ### Aliases: hotspotPlot > > ### ** Examples > > library(rtracklayer) > rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz") trying URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz' Warning in download.file(fp, filepath2[i]) : URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz': Timeout of 300 seconds was reached Error in download.file(fp, filepath2[i]) : cannot open URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz' Calls: readGFF ... <Anonymous> -> .normarg_input_filepath -> download.file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 6 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘geneXtendeR’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c annotate.c -o annotate.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_number.c -o extract_number.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_peaks.c -o extract_peaks.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-geneXtendeR/00new/geneXtendeR/libs ** R ** data *** moving datasets to lazyload DB ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geneXtendeR)
geneXtendeR.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(geneXtendeR) Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GO.db Loading required package: AnnotationDbi 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")'. > > test_check("geneXtendeR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ] > > proc.time() user system elapsed 218.528 20.134 239.171
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
name | user | system | elapsed | |
allPeakLengths | 0.052 | 0.007 | 0.061 | |
annotate | 24.160 | 0.628 | 30.247 | |
annotate_n | 0 | 0 | 0 | |
barChart | 24.101 | 0.950 | 30.044 | |
cumlinePlot | 23.785 | 0.859 | 100.887 | |
diffGO | 19.486 | 0.955 | 25.850 | |
distinct | 16.811 | 0.613 | 23.674 | |
gene_annotate | 19.691 | 0.535 | 24.840 | |
gene_lookup | 16.914 | 0.408 | 21.867 | |