Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:46 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 821/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geneXtendeR 1.30.0 (landing page) Bohdan Khomtchouk
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the geneXtendeR package: - 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 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: geneXtendeR |
Version: 1.30.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneXtendeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings geneXtendeR_1.30.0.tar.gz |
StartedAt: 2024-06-27 01:40:53 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 01:59:26 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 1113.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: geneXtendeR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneXtendeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings geneXtendeR_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.Rcheck' * using R version 4.4.1 (2024-06-14 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 'geneXtendeR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'geneXtendeR' version '1.30.0' * 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 whether package 'geneXtendeR' can be installed ... WARNING Found the following significant warnings: annotate.c:159:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] extract_peaks.c:202:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] See 'F:/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 11.3Mb sub-directories of 1Mb or more: data 5.7Mb 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 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 ... 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 5.7 MB without LazyDataCompression set See ยง1.1.6 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 for x64 is not available File 'F:/biocbuild/bbs-3.19-bioc/R/library/geneXtendeR/libs/x64/geneXtendeR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed meanPeakLengthPlot 67.31 2.57 72.39 hotspotPlot 50.15 1.21 53.60 cumlinePlot 37.98 0.66 40.64 linePlot 36.13 0.81 38.92 barChart 35.74 0.73 38.50 annotate 33.00 0.40 35.27 gene_annotate 31.00 0.40 33.35 makeWordCloud 30.62 0.74 33.32 meanPeakLength 30.27 0.47 32.64 diffGO 29.67 0.64 47.91 makeNetwork 29.34 0.56 32.03 plotWordFreq 28.76 0.67 31.33 distinct 28.92 0.36 31.18 gene_lookup 26.52 0.31 28.73 peakLengthBoxplot 26.20 0.41 28.69 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking package vignettes ... NOTE Package has 'vignettes' subdirectory but apparently no vignettes. Perhaps the 'VignetteBuilder' information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 7 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.Rcheck/00check.log' for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'geneXtendeR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c annotate.c -o annotate.o annotate.c: In function 'annotate': annotate.c:159:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 159 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 191 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 199 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 208 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 228 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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; | ^~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extract_peaks.c -o extract_peaks.o extract_peaks.c: In function 'extractpeaks': extract_peaks.c:202:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 202 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-geneXtendeR/00new/geneXtendeR/libs/x64 ** 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 ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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(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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 220.21 16.35 236.92
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
name | user | system | elapsed | |
allPeakLengths | 0.05 | 0.01 | 0.10 | |
annotate | 33.00 | 0.40 | 35.27 | |
annotate_n | 0 | 0 | 0 | |
barChart | 35.74 | 0.73 | 38.50 | |
cumlinePlot | 37.98 | 0.66 | 40.64 | |
diffGO | 29.67 | 0.64 | 47.91 | |
distinct | 28.92 | 0.36 | 31.18 | |
gene_annotate | 31.00 | 0.40 | 33.35 | |
gene_lookup | 26.52 | 0.31 | 28.73 | |
hotspotPlot | 50.15 | 1.21 | 53.60 | |
linePlot | 36.13 | 0.81 | 38.92 | |
makeNetwork | 29.34 | 0.56 | 32.03 | |
makeWordCloud | 30.62 | 0.74 | 33.32 | |
meanPeakLength | 30.27 | 0.47 | 32.64 | |
meanPeakLengthPlot | 67.31 | 2.57 | 72.39 | |
peakLengthBoxplot | 26.20 | 0.41 | 28.69 | |
peaksInput | 0.53 | 0.11 | 2.28 | |
peaksMerge | 0.27 | 0.00 | 0.28 | |
plotWordFreq | 28.76 | 0.67 | 31.33 | |
rat | 3.36 | 0.23 | 3.59 | |
samplepeaksinput | 0 | 0 | 0 | |