Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-22 11:36:38 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
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 251/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUScorrect 1.23.0 (landing page) Xiangyu Luo
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the BUScorrect package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUScorrect.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: BUScorrect |
Version: 1.23.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUScorrect_1.23.0.tar.gz |
StartedAt: 2024-05-20 22:49:55 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 22:53:03 -0400 (Mon, 20 May 2024) |
EllapsedTime: 188.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUScorrect.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUScorrect_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'BUScorrect/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BUScorrect' version '1.23.0' * 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 'BUScorrect' can be installed ... OK * 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) NEWS.Rd:12: Escaped LaTeX specials: \_ \_ \_ checkRd: (-1) BUSgibbs.Rd:34: Lost braces; missing escapes or markup? 34 | \code{a_inv_gamma}: the shape of the gamma prior for 1/sigma^2_{bg}; | ^ checkRd: (-1) BUSgibbs.Rd:35: Lost braces; missing escapes or markup? 35 | \code{b_inv_gamma}: the rate of the gamma prior for 1/sigma^2_{bg}; | ^ checkRd: (-1) BUSgibbs.Rd:36: Lost braces; missing escapes or markup? 36 | \code{a_tau0}: the shape of the gamma prior for 1/tau^2_{mu 0}; | ^ checkRd: (-1) BUSgibbs.Rd:39: Lost braces; missing escapes or markup? 39 | \code{tau_{mu1}}: the standard deviation of the normal prior of mu_{gk} (k >= 2) when the gene expression level in subtype k is different from that in subtype one. | ^ checkRd: (-1) BUSgibbs.Rd:52: Lost braces; missing escapes or markup? 52 | \item{tau_mu_zero}{The estimated tau_{mu 0}, which is the prior normal distribution's standard deviation of the subtype effects when there is no differential expression.} | ^ checkRd: (-1) BUSgibbs.Rd:57: Lost braces; missing escapes or markup? 57 | \item{gamma}{The estimated location batch effects, a G by B matrix, where gamma_{gb} is the ``location'' batch effect on gene g in the batch b. Note that the first column is zero as the first batch is taken as the reference batch without batch effects.} | ^ * 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 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-3.20-bioc/R/library/BUScorrect/libs/x64/BUScorrect.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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BUSgibbs 14.34 1.59 15.93 BUScorrect-package 14.50 0.94 15.44 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck/00check.log' for details.
BUScorrect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BUScorrect ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BUScorrect' ... ** 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 BUS_Cfunctions.c -o BUS_Cfunctions.o gcc -shared -s -static-libgcc -o BUScorrect.dll tmp.def BUS_Cfunctions.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-BUScorrect/00new/BUScorrect/libs/x64 ** R ** data ** 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 (BUScorrect)
BUScorrect.Rcheck/tests/runTests.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > BiocGenerics:::testPackage("BUScorrect") running the Gibbs sampler ... The Gibbs sampler takes: 0.001 mins calculating posterior means and posterior modes... calculating BIC... RUNIT TEST PROTOCOL -- Mon May 20 22:52:50 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : BUScorrect RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 6.45 0.45 6.89
BUScorrect.Rcheck/BUScorrect-Ex.timings
name | user | system | elapsed | |
BIC_BUS | 0.06 | 0.00 | 0.07 | |
BUScorrect-package | 14.50 | 0.94 | 15.44 | |
BUSexample_data | 0.02 | 0.00 | 0.02 | |
BUSgibbs | 14.34 | 1.59 | 15.93 | |
IG_index | 0.03 | 0.02 | 0.05 | |
Subtypes | 0.08 | 0.00 | 0.07 | |
adjusted_values | 0.06 | 0.02 | 0.08 | |
baseline_expression_values | 0.06 | 0.00 | 0.07 | |
calculate_EPSR_gamma | 0 | 0 | 0 | |
calculate_EPSR_mu | 0.02 | 0.00 | 0.01 | |
calculate_EPSR_sigma_sq | 0 | 0 | 0 | |
estimate_IG_indicators | 0.07 | 0.01 | 0.09 | |
location_batch_effects | 0.07 | 0.00 | 0.07 | |
postprob_DE | 0.09 | 0.00 | 0.09 | |
postprob_DE_thr_fun | 0.11 | 0.00 | 0.11 | |
print.BUSfits | 0.11 | 0.00 | 0.11 | |
scale_batch_effects | 0.09 | 0.00 | 0.09 | |
subtype_effects | 0.10 | 0.02 | 0.11 | |
summary.BUSfits | 0.12 | 0.00 | 0.13 | |
visualize_data | 0.03 | 0.00 | 0.03 | |