Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:41 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the geneXtendeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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 764/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geneXtendeR 1.25.0 (landing page) Bohdan Khomtchouk
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: geneXtendeR |
Version: 1.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings geneXtendeR_1.25.0.tar.gz |
StartedAt: 2023-02-28 03:59:22 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 04:16:38 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1036.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: geneXtendeR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings geneXtendeR_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.25.0’ * 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 ... WARNING Found the following significant warnings: annotate.c:106:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] annotate.c:116:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_number.c:98:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_number.c:108:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: data 5.8Mb 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed meanPeakLengthPlot 50.911 1.255 67.837 hotspotPlot 28.281 1.174 44.483 annotate 20.028 0.628 34.046 cumlinePlot 19.533 0.456 33.321 linePlot 19.230 0.573 34.783 barChart 18.622 0.417 33.184 diffGO 16.891 0.969 33.365 makeWordCloud 17.012 0.676 30.644 meanPeakLength 15.859 0.568 29.134 gene_annotate 15.699 0.588 30.318 makeNetwork 15.458 0.624 31.005 plotWordFreq 14.929 0.481 30.844 peakLengthBoxplot 14.296 0.457 35.327 distinct 14.162 0.517 27.866 gene_lookup 13.241 0.510 29.224 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘geneXtendeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c annotate.c -o annotate.o annotate.c: In function ‘annotate’: annotate.c:106:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fgets(varstr, 50000, varfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ annotate.c:116:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 116 | fgets(vcfstr, 10000, vcffp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c extract_number.c -o extract_number.o extract_number.c: In function ‘extractnumber’: extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable] 72 | long n_1; | ^~~ extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable] 66 | long j_1; | ^~~ extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable] 54 | char * pvcfcol5_5; | ^~~~~~~~~~ extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable] 53 | char * pvcfcol4_4; | ^~~~~~~~~~ extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable] 52 | char * pvcfcol3_3; | ^~~~~~~~~~ extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable] 51 | char * pvcfcol2_2; | ^~~~~~~~~~ extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable] 50 | char * pvcfcol1_1; | ^~~~~~~~~~ extract_number.c:98:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fgets(varstr, 50000, varfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ extract_number.c:108:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fgets(vcfstr, 10000, vcffp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c extract_peaks.c -o extract_peaks.o extract_peaks.c: In function ‘extractpeaks’: extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 107 | fgets(varstr, 50000, varfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fgets(vcfstr, 10000, vcffp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > 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, aperm, 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 215.866 6.234 221.932
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
name | user | system | elapsed | |
allPeakLengths | 0.044 | 0.000 | 0.049 | |
annotate | 20.028 | 0.628 | 34.046 | |
annotate_n | 0.000 | 0.000 | 0.001 | |
barChart | 18.622 | 0.417 | 33.184 | |
cumlinePlot | 19.533 | 0.456 | 33.321 | |
diffGO | 16.891 | 0.969 | 33.365 | |
distinct | 14.162 | 0.517 | 27.866 | |
gene_annotate | 15.699 | 0.588 | 30.318 | |
gene_lookup | 13.241 | 0.510 | 29.224 | |
hotspotPlot | 28.281 | 1.174 | 44.483 | |
linePlot | 19.230 | 0.573 | 34.783 | |
makeNetwork | 15.458 | 0.624 | 31.005 | |
makeWordCloud | 17.012 | 0.676 | 30.644 | |
meanPeakLength | 15.859 | 0.568 | 29.134 | |
meanPeakLengthPlot | 50.911 | 1.255 | 67.837 | |
peakLengthBoxplot | 14.296 | 0.457 | 35.327 | |
peaksInput | 0.249 | 0.027 | 0.288 | |
peaksMerge | 0.158 | 0.008 | 0.164 | |
plotWordFreq | 14.929 | 0.481 | 30.844 | |
rat | 3.965 | 0.312 | 4.277 | |
samplepeaksinput | 0.008 | 0.000 | 0.009 | |