Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1610/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qsea 1.31.0 (landing page) Matthias Lienhard
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the qsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsea.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: qsea |
Version: 1.31.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings qsea_1.31.0.tar.gz |
StartedAt: 2024-08-16 03:59:39 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 04:05:04 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 325.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qsea.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings qsea_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/qsea.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 'qsea/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'qsea' version '1.31.0' * 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 whether package 'qsea' can be installed ... WARNING Found the following significant warnings: lm.c:63:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 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 ... NOTE checkRd: (-1) fitNBglm.Rd:16: Lost braces 16 | dQuote{log} link function is implemented. } | ^ checkRd: (-1) fitNBglm.Rd:19: Lost braces 19 | Allowed values are dQuote{region_wise} for independent window wise estimates, | ^ checkRd: (-1) fitNBglm.Rd:20: Lost braces 20 | dQuote{common} for a single estimate for all windows, | ^ checkRd: (-1) fitNBglm.Rd:21: Lost braces 21 | dQuote{cutAtQuantiles} for window wise estimates trimmed at the 25\% and 75\% | ^ checkRd: (-1) fitNBglm.Rd:23: Lost braces 23 | or dQuote{initial} for using the dispersion parameters provided with the | ^ checkRd: (-1) plotCNV.Rd:20: Lost braces 20 | \item{dist}{distance measure for clustering. dQuote{euclid}ian | ^ checkRd: (-1) plotCNV.Rd:21: Lost braces 21 | or dQuote{cor}relation based (1-cor)} | ^ * 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 R/sysdata.rda ... 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-3.20-bioc/R/library/qsea/libs/x64/qsea.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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed addNewSamples 16.25 1.09 19.30 addPatternDensity 9.84 0.52 10.33 addCNV 8.26 0.36 9.05 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck/00check.log' for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'qsea' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o lm.c: In function 'Cdqrls': lm.c:63:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 63 | error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lm.c:31:38: note: in definition of macro '_' 31 | #define _(String) dgettext ("stats", String) | ^~~~~~ lm.c:63:50: note: format string is defined here 63 | error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"), | ~^ | | | int | %lld gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-qsea/00new/qsea/libs/x64 ** R ** inst ** preparing 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 (qsea)
qsea.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(qsea) > > test_check("qsea") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] > > proc.time() user system elapsed 13.67 0.73 14.53
qsea.Rcheck/qsea-Ex.timings
name | user | system | elapsed | |
addCNV | 8.26 | 0.36 | 9.05 | |
addContrast | 1.50 | 0.01 | 1.51 | |
addCoverage | 3.26 | 0.16 | 3.44 | |
addEnrichmentParameters | 0.55 | 0.06 | 0.61 | |
addLibraryFactors | 0.95 | 0.09 | 1.06 | |
addNewSamples | 16.25 | 1.09 | 19.30 | |
addOffset | 0.36 | 0.02 | 0.37 | |
addPatternDensity | 9.84 | 0.52 | 10.33 | |
createQseaSet | 0.17 | 0.09 | 0.28 | |
example | 0.25 | 0.02 | 0.27 | |
fitNBglm | 0.95 | 0.06 | 1.01 | |
getPCA | 0.65 | 0.01 | 0.66 | |
isSignificant | 1.40 | 0.07 | 1.47 | |
makeTable | 1.53 | 0.14 | 1.67 | |
normMethod | 0 | 0 | 0 | |
plotCNV | 0.30 | 0.01 | 0.31 | |
plotCoverage | 0.91 | 0.03 | 0.94 | |
plotEnrichmentProfile | 0.48 | 0.03 | 0.51 | |
plotPCA | 0.52 | 0.04 | 0.55 | |
qseaGLM-class | 0 | 0 | 0 | |
qseaPCA-class | 0 | 0 | 0 | |
qseaSet-class | 0 | 0 | 0 | |
regionStats | 0.64 | 0.01 | 0.66 | |