Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1936/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqTools 1.40.0 (landing page) Wolfgang Kaisers
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the seqTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.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: seqTools |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqTools_1.40.0.tar.gz |
StartedAt: 2024-12-20 05:25:31 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:25:59 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 28.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: seqTools.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqTools_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seqTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘seqTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqTools’ version ‘1.40.0’ * 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 ‘seqTools’ can be installed ... WARNING Found the following significant warnings: seqTools.c:851:93: warning: format ‘%u’ expects a matching ‘unsigned int’ argument [-Wformat=] seqTools.c:3296:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] seqTools.c:3306:73: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] See ‘/home/biocbuild/bbs-3.20-bioc/meat/seqTools.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘kmerSvd’ Undocumented S4 methods: generic 'kmerSvd' and siglist 'Fastqq' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/libs/seqTools.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) 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 files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata’, resetting * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ Running ‘test_seqTools.r’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs See ‘/home/biocbuild/bbs-3.20-bioc/meat/seqTools.Rcheck/00check.log’ for details.
seqTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL seqTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘seqTools’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c seqTools.c -o seqTools.o seqTools.c: In function ‘count_genome_Kmers’: seqTools.c:851:93: warning: format ‘%u’ expects a matching ‘unsigned int’ argument [-Wformat=] 851 | error("[count_genome_Kmers] character mismatch at position %u!"); | ~^ | | | unsigned int seqTools.c: In function ‘scale_kmer_matrix’: seqTools.c:3296:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] 3296 | error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale); | ~^ ~~~~~ | | | | int double | %f seqTools.c:3306:73: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] 3306 | error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale); | ~^ ~~~~~ | | | | int double | %f gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o seqTools.so seqTools.o -lm -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-seqTools/00new/seqTools/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: In fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (seqTools)
seqTools.Rcheck/tests/test-all.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Load prerequisites > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > library(seqTools) Loading required package: zlibbioc Warning message: In fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Initialize example data > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > basedir<-system.file("extdata",package="seqTools") > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Run tests > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > filename <- "test_seqTools.R" > basedir <- system.file("extdata", package = "seqTools") > load(file.path(basedir,"test_res.RData")) > > > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## kmerCount.fastqq > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l5_N.fq' done. > if(!identical(kmerCount(fq), kmer_l5_N)) + stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!") > > fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l6.fq' done. > if(!identical(kmerCount(fq), kmer_l6)) + stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!") > > fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l6_multi_line.fq' done. > if(!identical(kmerCount(fq), kmer_l6_ml)) + stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!") > > fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l10_20_40.fq' done. > if(!identical(kmerCount(fq), kmer_l10_20)) + stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!") > > fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l10_atcg.fq' done. > if(!identical(kmerCount(fq), kmer_l10_atcg)) + stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!") > > fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2) [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/seqTools/extdata/test_l10_ATCGN.fq' done. > if(!identical(kmerCount(fq), kmer_l10_ATCGN)) + stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!") > > # Counting k-mers on linux ('\n') and equal windows ('\r\n') > # formatted FASTQ file should give equal results > # fq<-fastqq(file.path(basedir, c("test_l4.fq", "test_win.fq")), k = 2) > # kc <- kmerCount(fq) > # if(!all(kc[,1]==kc[,2])) > # stop("[kmerCount.fastqq] test_l4: kmerCount unequal to test_win.fq") > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## ascii2char, char2ascii > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > if(!identical(ascii2char(97:101, multiple = FALSE), "abcde")) + stop("[ascii2char] Test 1 '", filename, "' FAILED!") > > if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5])) + stop("[ascii2char] Test 2 '", filename, "' FAILED!") > > if(!identical(ascii2char(char2ascii("abcde")), "abcde")) + stop("[ascii2char] Test 3 '", filename, "' FAILED!") > > if(!identical(char2ascii("abcde"), 97:101)) + stop("[char2ascii] Test 1 '", filename, "' FAILED!") > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## END OF FILE > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > > proc.time() user system elapsed 0.200 0.050 0.238
seqTools.Rcheck/tests/test_seqTools.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Load prerequisites > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > library(seqTools) Loading required package: zlibbioc Warning message: In fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Initialize example data > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > basedir<-system.file("extdata",package="seqTools") > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## Run tests > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > filename <- "test_seqTools.R" > basedir <- system.file("extdata", package = "seqTools") > load(file.path(basedir,"test_res.RData")) > > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## countDnaKmers > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT)) + stop("[countDnaKmers] Test 1 '", filename, "' FAILED!") > > if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one)) + stop("[countDnaKmers] Test 2 '", filename, "' FAILED!") > > if(!identical( + countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC)) + stop("[countDnaKmers] Test 3 '", filename, "' FAILED!") > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## revCountDnaKmers > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > if(!identical( + revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT)) + stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!") > > > > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > ## END OF FILE > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## > > proc.time() user system elapsed 0.199 0.051 0.238
seqTools.Rcheck/seqTools-Ex.timings
name | user | system | elapsed | |
ascii2char | 0 | 0 | 0 | |
cbDistMatrix | 0.003 | 0.000 | 0.003 | |
countDnaKmers | 0 | 0 | 0 | |
countFastaKmers | 0.001 | 0.000 | 0.027 | |
countGenomeKmers | 0.001 | 0.000 | 0.000 | |
countSpliceKmers | 0 | 0 | 0 | |
kMerIndex | 0 | 0 | 0 | |
phredTable | 0.002 | 0.000 | 0.003 | |
revCountDnaKmers | 0 | 0 | 0 | |
simFastqqRunTimes | 0 | 0 | 0 | |
sim_fq | 0 | 0 | 0 | |
writeFai | 0 | 0 | 0 | |
writeSimContFastq | 0 | 0 | 0 | |
writeSimFastq | 0.000 | 0.001 | 0.001 | |